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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 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Formulation and solution approach for calibrating activity-based travel demand model-system via microsimulation

This study addresses the problem of calibrating utility-maximizing nested logit activity-based travel demand model-systems. After estimation, it is common practice to use aggregate measurements to calibrate the estimated model-system’s parameters prior to their application in transportation planning, policy making, and operations. However, calibration of activity-based model-systems has received much less attention. Existing calibration approaches are myopic heuristics in the sense that they do not consider the fundamental inter-dependencies among choice-models and do not have a systematic way to adjust model parameters. Also, other purely simulation-based approaches do not perform well in large-scale applications. In this study, we focus on utility-maximizing nested logit activity-based model-systems and calibrating aggregate statistics such as activity shares, mode shares, time-dependent & mode-specific OD flows, and time-dependent & mode-specific sensor counts. We formulate the calibration problem as a simulation-based optimization problem and propose a stochastic gradient-based solution procedure to solve it. The solution procedure relies on microsimulation to calculate expectations of the aggregate statistics of interest to the calibration problem. Additionally, we derive approximate analytical expressions for the gradient of the objective function —that are evaluated through microsimulation on mini-batches of the population. The proposed solution procedure is sensitive to the fundamental structure of the activity-based model-system and is non-myopic in considering the dependencies across its model components. The formulated optimization problem is non-convex, highly nonlinear, and potentially has multiple-minima. Lastly, we show —through a real-world application— that the proposed solution procedure outperforms other state-of-the-art purely simulation-based optimization approaches in terms of computational efficiency, stability, and convergence. We also compare various gradient-based solution algorithms to determine the best algorithm to update the parameters. This work has the potential to facilitate wider and easier application of activity-based model-systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Investigating drivers of microbial activity and respiration in a forested bog

Northern peatlands store nearly one-third of terrestrial carbon (C) stocks while covering only 3% of the global landmass; nevertheless, the drivers of C cycling in these often-waterlogged ecosystems are different from those that control C dynamics in upland forested soils. To explore how multiple abiotic and biotic characteristics of bogs interact to shape microbial activity in a northern, forested bog, we added a labile C tracer ( 13 C-labeled starch) to in situ peat mesocosms and correlated heterotrophic respiration with natural variation in several microbial predictor variables, such as enzyme activity and microbial biomass, as well as with a suite of abiotic variables and proximity to vascular plants aboveground. We found that peat moisture content was positively correlated with respiration and microbial activity, even when moisture levels exceeded total saturation, suggesting that access to organic matter substrates in drier environments may be limiting for microbial activity. Proximity to black spruce trees decreased total and labile heterotrophic respiration. This negative relationship may reflect the influence of tree evapotranspiration and peat shading effects; i.e., microbial activity may decline as peat dries and cools near trees. Here, we isolated the response of heterotrophic respiration to explore the variation in, and interactions among, multiple abiotic and biotic drivers that influence microbial activity. This approach allowed us to reveal the relative influence of individual drivers on C respiration in these globally important C sinks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bulk vs Intrinsic Activity of NiFeO x Electrocatalysts in the Oxygen Evolution Reaction: The Influence of Catalyst Loading, Morphology, and Support Material

We used a combination of ultrahigh vacuum surface science techniques, X-ray spectroscopy, electrochemistry, and density functional theory (DFT), to characterize the influence of catalyst morphology, loading/coverage, and substrate material on the bulk (all atoms) and intrinsic (electrochemically accessible atoms) activity of NiFeO x electrocatalysts in the oxygen evolution reaction (OER). NiFeO x catalysts were grown on both Au(111) and highly oriented pyrolytic graphite (HOPG) electrodes. DFT predicted Fe edge-site atoms at the NiFeO x /Au(111) interface to be the most thermodynamically favorable reaction center, and X-ray absorption spectroscopy data indicated small NiFeO x catalyst particles on Au(111) contained a high population of OER active Fe edge-site atoms. However, restructuring of the Au(111) surface due to repeated oxidation and reduction cycles of the OER CV measurements encapsulated small NiFeO x nanoparticles at catalyst loadings below ~1.5 nmol metal /cm 2 , passivated catalyst edges and reduced bulk OER activity of Au-supported NiFeO x compared with HOPG-supported ones. Analysis of intrinsic activity revealed that the Au(111) support strongly benefited electrochemically accessible NiFeO x atoms, and we observed a 2–3 fold activity enhancement compared with HOPG-supported catalysts for loadings above ~1 nmol metal /cm 2 . Overall, evaluating bulk vs intrinsic activity and identifying loading/coverage-dependent support effects is important for accurately probing fundamental interfacial chemistry, choosing suitable catalyst loadings and supports, and optimizing system parameters to maximize the performance of electrocatalyst systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Free-Energy Landscapes and Surface Dynamics in Methane Activation on Ni(511) via Machine Learning and Enhanced Sampling

Methane activation on stepped Ni(511) surfaces involves the rearrangement of surface atoms as the chemical reaction proceeds. This process is particularly sensitive to temperature. Using machine-learned interatomic potentials (MLIPs) coupled with enhanced sampling techniques, we investigate the activation of methane under realistic operando conditions. Our analysis reveals that methane dissociation occurs predominantly at step-edge nickel atoms. As CH x (where x = 3 or 4) species bind to additional surface nickel atoms, their reduced mobility leads to entropic penalties that suppress certain configurations and transition states. This is reflected in the underlying free energy surfaces, where configurations such as methyl binding to hollow sites and activation routes involving two nickel atoms become unfavorable as temperature increases. At elevated temperatures, methane activation extends from step-edge sites to terrace regions because of reduced free-energy barriers and enhanced surface dynamics. By decomposing the free-energy into enthalpic and entropic contributions, we uncover temperature-dependent shifts in the preferences of methane for the relevant active sites and arrive at a detailed molecular picture of methane activation.

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

Composition, Activity, and Stability of IrO x Oxygen Evolution Reaction Electrocatalysts

The oxygen evolution reaction (OER) is integral to several electrochemical energy conversion and storage technologies, including carbon dioxide reduction to value added fuels, nitrogen reduction to ammonia, reversible fuel cells, rechargeable metal−air batteries, and water electrolysis to produce hydrogen. Iridium oxide (IrO x ) is widely recognized as the benchmark OER catalyst for acidic environments. Despite widespread use of IrO x catalysts, most notably in proton-exchange membrane water electrolyzers (PEMWEs), a comprehensive understanding of the physicochemical properties of commercial catalysts and the impact of these properties on both the activity and stability of these catalysts is lacking. Here, we study commercial IrO x catalysts with different physicochemical properties, three nominally considered amorphous and three rutile, to elucidate how structural and compositional variations affect OER activity and stability. Utilizing standardized aqueous electrochemical protocols, time-resolved dissolution quantification using inductively-coupled plasma mass spectrometry, and physicochemical characterization, including multiple synchrotron X-ray techniques, we systematically correlate catalyst properties with OER performance and degradation behavior aided by principal component analysis (PCA). Our results demonstrate the general trend of amorphous IrO x having higher intrinsic activity but limited stability and crystalline rutile IrO 2 having lower activity but enhanced stability against dissolution. The trends within the amorphous and rutile catalyst groups correlate with inherent material properties, including phase composition and structure, crystallinity, particle size, surface area, and surface structure/chemistry. Notably, we identify a rutile catalyst with the largest crystallite/ domain sizes, moderate surface area, a small fraction of hydrous phase, and a favorable pore structure (trimodal distributions of pore sizes ranging from 2−5 nm) that exhibits the best balance between activity and stability among the six catalysts studied here. These findings illustrate a fundamental structure-governed trade-off between activity and stability and highlight the critical role of surface chemistry modification and structure engineering in IrO x catalyst optimization.

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

Simultaneous Activation of CH4 and CO2 for Concerted C-C Coupling at the Oxide-Oxide Interfaces

Catalytic conversion of CO2 and CH4 to value-added platform chemicals via the direct C-C coupling provides one of the most effective routes that not only address global climate change but also alleviate the dependency on traditional fossil fuels. Herein, three oxide-on-oxide catalysts that can realize direct C-C coupling on the basis of simultaneous activation of CH4 and CO2 were investigated using density functional theory (DFT) calculations. With the formation of oxide-on-oxide interfacial sites between the substrate (In2O3) and dispersed oxides ((ZnO)3, (ZrO2)3, or Ga2O3), it is found that CO2 can be activated at the defective site of In2O3 while the C-H bond of CH4 can be simultaneously activated at the M-O pair of the supported metal oxide. In contrast to the Eley-Rideal mechanism that C-C coupling of CO2 and CH3 stabilized on Zn-doped ceria follows, the formation of a Zn-C-C-O transition state at the active centers originates from a Langmuir-Hinshelwood mechanism where the activated CO2 also enhances the dissociative adsorption of CH4. There is a linear relationship between the C-C coupling reaction energy/activation barrier and CH4 dissociation energy. The results indicate that dissociative adsorption of CH4 plays a dominant role in the direct C-C coupling, whereas the adsorption/activation of CO2 is less significant. DFT calculation results of CH4 and CO2 to acetic acid on the (ZnO)3/In2O3 catalyst surface indicates that the C-C coupling step is the kinetically most relevant step. Compared with Ga2O3/In2O3 and (ZrO2)3/In2O3 catalyst surfaces, (ZnO)3/In2O3(110) is more active for the acetic acid formation. The present work provides new mechanistic insights into the direct C-C coupling of CH4 and CO2, which would be useful to design more efficient catalyst.

CH4 activation, C-C coupling, supported oxides, In↗
DOE OSTI2021

Click-Chemistry-Based Free Azide versus Azido Sugar Detection Enables Rapid In Vivo Screening of Glycosynthase Activity

Engineering of carbohydrate-active enzymes such as glycosynthases to enable chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable ultrahigh-throughput screening methods capable of robustly detecting either starting substrates or end-products of the glycosidic bond formation reaction. Currently, there are limited screening methods available for rapid and highly sensitive single-cell-based screening of glycosynthase enzymes employing azido sugars as activated donor glycosyl substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides as substrates versus free inorganic azides as reaction products that facilitated an ultrahigh-throughput in vivo single-cell-based assay of glycosynthase activity. This assay was developed based on the distinct differences observed in relative fluorescence intensity of the triazole-containing fluorophore product formed during the click-chemistry reaction of organic glycosyl azides versus inorganic azides. This discovery formed the basis for proof of concept validation of a directed evolution methodology for screening and sorting glycosynthase mutants capable of synthesis of targeted fucosylated oligosaccharides. Our screening approach facilitated fluorescence-activated cell sorting of an error-prone polymerase chain reaction-based mutant library of fucosynthases expressed in Escherichia coli to identify several novel mutants that showed increased activity for ß-fucosyl azide-activated donor sugars toward desired acceptor sugars (e.g., pNP-xylose and lactose). Finally, we discuss avenues for improving this proof of concept in vivo assay method to identify better glycosynthase mutants and further demonstrate the broader applicability of this screening methodology for synthesis of bespoke glycans.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Band-Gap Energy as a Descriptor of Catalytic Activity for Propene Oxidation over Mixed Metal Oxide Catalysts

The development of a descriptor or descriptors that can relate the activity of catalysts to their physical properties is a major objective of catalysis research. In this study, we have found that the apparent activation energy for propene oxidation to acrolein over scheelite-structured, multicomponent, mixed metal oxides (Bi 3 FeMo 2 O 12 , Bi 2 Mo 2.5 W 0.5 O 12 , and Bi 1- x /3 V 1- x Mo x O 4 , where 0 x 1) correlates with the band gap of the catalyst measured at reaction temperature. We show through theoretical analysis of the energy components comprising the activation energy why the band-gap energy is the primary component dependent on catalyst composition and, hence, why one should expect the activation energy for propene oxidation to correlate with the band-gap energy. We also demonstrate that the change in band-gap energy with composition arises from the interplay between the sizes and energies of the V 3d, Fe 3d, Mo 4d, and W 5d orbitals, which give rise to the lowest unoccupied crystal orbitals. Both the utility of the band-gap energy as a descriptor for catalytic activity and the role of orbital overlap in determining the band gap are likely to be general features in mixed metal oxide oxidation catalysts, enabling the rational design of catalysts with greater activity for oxidation reactions.

activation energy↗
DOE OSTI2021

Increasing Iridium Oxide Activity for the Oxygen Evolution Reaction with Hafnium Modification

Synthesis and implementation of highly active, stable, and affordable electrocatalysts for the oxygen evolution reaction (OER) is a major challenge in developing energy efficient and economically viable energy conversion devices such as electrolyzers, rechargeable metal-air batteries, and regenerative fuel cells. The current benchmark electrocatalyst for OER is based on iridium oxide (IrO x ) due to its superior performance and excellent stability. However, large scale applications using IrO x are impractical due to its low abundance and high cost. In this work, we report a highly active hafnium-modified iridium oxide (IrHf x O y ) electrocatalyst for OER. The IrHf x O y electrocatalyst demonstrated ten times higher activity in alkaline conditions (pH = 11) and four times higher activity in acid conditions (pH = 1) than a IrO x electrocatalyst. The highest intrinsic mass activity of the IrHf x O y catalyst in acid conditions was calculated as 6950 A gIrO x -1 at an overpotential (η) of 0.3 V. Combined studies utilizing operando surface enhanced Raman spectroscopy (SERS) and DFT calculations revealed that the active sites for OER are the Ir-O species for both IrO x and IrHf x O y catalysts. The presence of Hf sites leads to more negative charge states on nearby O sites, and shortening the bond lengths of Ir-O, and lowering free energies for OER intermediates to accelerate the OER process.

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

Dynamics and activation of membrane-bound B cell receptor assembly

B-cell receptor (BCR) complexes are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes have been published that validates the asymmetric organization of the BCR complex. Here, we carry out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identify two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding causes increased flexibility in regions distal to the antigen binding site. Second, antigen binding alters the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements lead to changes in localized lipid composition. Our work indirectly supports the conformational-change induced models of BCR activation and contributes to the understanding of the antigen-dependent activation mechanism of BCRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

From cellulose to 1,2,4-benzenetriol via catalytic degradation over a wood-based activated carbon catalyst

In this study, spherical P-doped activated carbon (CSP) was obtained from poplar bark by microwave carbonization with phosphoric acid as the dopant and activating agent. Phosphorus bonded with four oxygen atoms to form a phosphate-like structure rather than directly bonding with C atoms in CSP; such groups can provide Lewis acid active sites with moderately strong acidity. The Lewis acid and total acid content increased with increasing phosphoric acid doping ratio. The use of phosphoric acid as an activating agent promotes the formation of a developed porous structure. CSP 1 (mass ratio of raw material to acid = 1 : 1) had a specific surface area of 1115 m 2 g –1 with developed micro–mesoporous structures, mainly micropores. Investigation of the activity of CSP in catalytic cellulose hydrolysis during hydrothermal degradation showed that Brønsted acid sites promote hydrolysis and dehydration of cellulose, Lewis acid sites promote subsequent reactions such as isomerization, rearrangement, and oligomerization, and the developed pores can provide reaction sites and facilitate reactant transportation. The optimal reaction conditions, i.e. , 1 h at 230 °C and 1 MPa with CSP 1 (0.4 g) as the catalyst, gave a cellulose conversion of >99.9%, with 42.30% selectivity for 1,2,4-benzenetriol. This study provides an effective method for preparing 1,2,4-benzenetriol from cellulose with biomass-based activated carbon as the catalyst, which enables green synthesis of 1,2,4-benzenetriol and promotes the use of biomass waste resources.

1,2,4-benzenetriol↗
DOE OSTI2024

Microscopic origin of tunable assembly forces in chiral active environments

Across a variety of spatial scales, from nanoscale biological systems to micron-scale colloidal systems, equilibrium self-assembly is entirely dictated by—and therefore limited by—the thermodynamic properties of the constituent materials. In contrast, nonequilibrium materials, such as self-propelled active matter, expand the possibilities for driving the assemblies that are inaccessible in equilibrium conditions. Recently, a number of works have suggested that active matter drives or accelerates self-organization, but the emergent interactions that arise between solutes immersed in actively driven environments are complex and poorly understood. Here, we analyze and resolve two crucial questions concerning actively driven self-assembly: (i) how, mechanistically, do active environments drive self-assembly of passive solutes? (ii) Under which conditions is this assembly robust? We employ the framework of odd hydrodynamics to theoretically explain numerical and experimental observations that chiral active matter, i.e., particles driven with a directional torque, produces robust and long-ranged assembly forces. Overall, these developments constitute an important step towards a comprehensive theoretical framework for controlling self-assembly in nonequilibrium environments.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Improving the mechanical properties of Zr-based bulk metallic glass by controlling the activation energy for β-relaxation through plastic deformation

The mechanism of plastic deformation in bulk metallic glasses (BMGs) is widely believed to be based on a shear transformation zone (STZ). This model assumes that a shear-induced atomic rearrangement occurs at local clusters that are a few to hundreds of atoms in size. It was recently postulated that the potential energy barrier for STZ activation, W{sub STZ}, calculated using the cooperative shear model, is equivalent to the activation energy for β-relaxation, E{sub β}. This result suggested that the fundamental process for STZ activation is the mechanically activated β-relaxation. Since the E{sub β} value and the glass transition temperature T{sub g} of BMGs have a linear relation, that is, because E{sub β} ≈ 26RT{sub g}, the composition of the BMG determines the ease with which the STZ can be activated. Enthalpy relaxation experiments revealed that the BMG Zr{sub 50}Cu{sub 40}Al{sub 10} when deformed by high-pressure torsion (HPT) has a lower E{sub β} of 101 kJ/mol. The HPT-processed samples accordingly exhibited tensile plastic elongation (0.34%) and marked decreases in their yield strength (330 MPa). These results suggest that mechanically induced structural defects (i.e., the free volume and the anti-free volume) effectively act to reduce W{sub STZ} and increase the number of STZs activated during tensile testing to accommodate the plastic strain without requiring a change in the composition of the BMG. Thus, this study shows quantitatively that mechanically induced structural defects can overcome the compositional limitations of E{sub β} (or W{sub STZ}) and result in improvements in the mechanical properties of the BMG.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Removal of Ni(II), Zn(II) and Pb(II) ions from single metal aqueous solution using rice husk-based activated carbon

An attempt was made to investigate the potential of rice husk-based activated carbon as an alternative low-cost adsorbent for the removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Rice husk-based activated carbon was prepared via treatment of rice husk with NaOH followed by the carbonization process at 400°C for 2 hours. Three samples, i.e. raw rice husk, rice husk treated with NaOH and rice husk-based activated carbon, were analyzed for their morphological characteristics using field-emission scanning electron microscope/energy dispersive X-ray (FESEM/EDX). These samples were also analyzed for their carbon, hydrogen, nitrogen, oxygen and silica contents using CHN elemental analyzer and FESEM/EDX. The porous properties of rice husk-based activated carbon were determined by Brunauer-Emmett-Teller (BET) surface area analyzer, and its surface area and pore volume were 255 m{sup 2}/g and 0.17 cm{sup 2}/g, respectively. The adsorption studies for the removal of Ni(II), Zn(II) and Pb(II) ions from single metal aqueous solution were carried out at a fixed initial concentration of metal ion (150 ppm) with variation amount of adsorbent (rice husk-based activated carbon) as a function of varied contact time at room temperature. The concentration of each metal ion was analyzed using atomic absorption spectrophotometer (AAS). The results obtained from adsorption studies indicate the potential of rice husk as an economically promising precursor for the preparation of activated carbon for removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Isotherm and kinetic model analyses suggested that the experimental data of adsorption studies fitted well with Langmuir, Freundlich and second-order kinetic models.

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

Coupling of Ca 2+ and voltage activation in BK channels through the αB helix/voltage sensor interface

Large-conductance Ca 2+ and voltage-activated K + (BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is composed of a voltage sensor domain (VSD), a central pore-gate domain, and a large cytoplasmic domain (CTD) that contains the Ca 2+ sensors. While it is known that BK channels are activated by voltage and Ca 2+ , and that voltage and Ca 2+ activations interact, less is known about the mechanisms involved. In this work we explore these mechanisms by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the Horrigan, Cui, and Aldrich model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca 2+ activation for both Ca 2+ bowl and RCK1 Ca 2+ sites, suggesting that both high-affinity Ca 2+ sites transduce their effect, at least in part, through the αB helix. Mg 2+ activation also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to wild type, without other notable differences in the CTD, indicating that structural changes from the mutation were confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca 2+ binding and voltage depolarization to pore opening and that shared Ca 2+ and voltage transduction pathways involving the αB helix may be involved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Revealing the structure of a catalytic combustion active-site ensemble combining uniform nanocrystal catalysts and theory insights

Supported metal catalysts are extensively used in industrial and environmental applications. To improve their performance, it is crucial to identify the most active sites. This identification is, however, made challenging by the presence of a large number of potential surface structures that complicate such an assignment. Often, the active site is formed by an ensemble of atoms, thus introducing further complications in its identification. Being able to produce uniform structures and identify the ones that are responsible for the catalyst performance is a crucial goal. Here, we utilize a combination of uniform Pd/Pt nanocrystal catalysts and theory to reveal the catalytic active-site ensemble in highly active propene combustion materials. Using colloidal chemistry to exquisitely control nanoparticle size, we find that intrinsic rates for propene combustion in the presence of water increase monotonically with particle size on Pt-rich catalysts, suggesting that the reaction is structure dependent. We also reveal that water has a near-zero or mildly positive reaction rate order over Pd/Pt catalysts. Theory insights allow us to determine that the interaction of water with extended terraces present in large particles leads to the formation of step sites on metallic surfaces. These specific step-edge sites are responsible for the efficient combustion of propene at low temperature. This work reveals an elusive geometric ensemble, thus clearly identifying the active site in alkene combustion catalysts. These insights demonstrate how the combination of uniform catalysts and theory can provide a much deeper understanding of active-site geometry for many applications

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

Asymmetric fluctuations and self-folding of active interfaces

We study the structure and dynamics of the interface separating a passive fluid from a microtubule-based active fluid. Turbulent-like active flows power giant interfacial fluctuations, which exhibit pronounced asymmetry between regions of positive and negative curvature. Experiments, numerical simulations, and theoretical arguments reveal how the interface breaks up the spatial symmetry of the fundamental bend instability to generate local vortical flows that lead to asymmetric interface fluctuations. The magnitude of interface deformations increases with activity: In the high activity limit, the interface self-folds invaginating passive droplets and generating a foam-like phase, where active fluid is perforated with passive droplets. These results demonstrate how active stresses control the structure, dynamics, and break-up of soft, deformable, and reconfigurable liquid–liquid interfaces.

active fluid↗
DOE OSTI2015

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: Biochemical and Structural Studies

Members of the Swi2/Snf2 (switch/sucrose non-fermentable) family rely on their ATPase activity to mobilize nucleic acid-protein complexes for gene expression. In bacteria, RapA is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein that mediates RNAP recycling during transcription. It is known that the ATPase activity of RapA is stimulated by its interaction with RNAP. It is not known, however, how the RapA-RNAP interaction activates the enzyme. Previously, we determined the crystal structure of RapA. The structure revealed the dynamic nature of its N-terminal domain (Ntd), which prompted us to elucidate the solution structure and activity of both the full-length protein and its Ntd-truncated mutant (RapAΔN). Here, we report the ATPase activity of RapA and RapAΔN in the absence or presence of RNAP and the solution structures of RapA and RapAΔN either ligand-free or in complex with RNAP. Determined by small-angle x-ray scattering, the solution structures reveal a new conformation of RapA, define the binding mode and binding site of RapA on RNAP, and show that the binding sites of RapA and σ70 on the surface of RNAP largely overlap. We conclude that the ATPase activity of RapA is inhibited by its Ntd but stimulated by RNAP in an allosteric fashion and that the conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. These and previous findings outline the functional cycle of RapA, which increases our understanding of the mechanism and regulation of Swi2/Snf2 proteins in general and of RapA in particular. The new structural information also leads to a hypothetical model of RapA in complex with RNAP immobilized during transcription.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗