Search NASA⌕ Search

SEARCH · Search NASA

Results for “INTERMEDIATE COUPLING”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases

ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein–protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.

Chemistry↗
DOE OSTI2022

Quantum Simulation of Molecular Electronic States with a Transcorrelated Hamiltonian: Higher Accuracy with Fewer Qubits

Simulation of electronic structure is one of the most promising applications on noisy intermediate-scale quantum (NISQ) era devices. However, NISQ devices suffer from a number of challenges like limited qubit connectivity, short coherence times, and sizable gate error rates. Thus, desired quantum algorithms should require shallow circuit depths and low qubit counts to take advantage of these devices. Here, we attempt to reduce quantum resource requirements for molecular simulations on a quantum computer while maintaining the desired accuracy with the help of classical quantum chemical theories of canonical transformation and explicit correlation. In this work, compact ab initio Hamiltonians are generated classically, in the second quantized form, through an approximate similarity transformation of the Hamiltonian with (a) an explicitly correlated two-body unitary operator with generalized pair excitations that remove the Coulombic electron–electron singularities from the Hamiltonian and (b) a unitary one-body operator to efficiently capture the orbital relaxation effects required for accurate description of the excited states. The resulting transcorrelated Hamiltonians are able to describe both the ground and the excited states of molecular systems in a balanced manner. Using the variational quantum eigensolver (VQE) method based on the unitary coupled cluster with singles and doubles (UCCSD) ansatz and only a minimal basis set (ANO-RCC-MB), we demonstrate that the transcorrelated Hamiltonians can produce ground state energies comparable to the reference CCSD energies with the much larger cc-pVTZ basis set. This leads to a reduction in the number of required CNOT gates by more than 3 orders of magnitude for the chemical species studied in this work. Furthermore, using the quantum equation of motion (qEOM) formalism in conjunction with the transcorrelated Hamiltonian, we are able to reduce the deviations in the excitation energies from the reference EOM-CCSD/cc-pVTZ values by an order of magnitude. In conclusion, the transcorrelated Hamiltonians developed here are Hermitian and contain only one- and two-body interaction terms and thus can be easily combined with any quantum algorithm for accurate electronic structure simulations.

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

Plasmonic lens enhanced mid-infrared quantum cascade detector

We demonstrate monolithic integrated quantum cascade detectors enhanced by plasmonic lenses. Surface normal incident mid-infrared radiation is coupled to surface plasmon polaritons guided to and detected by the active region of the detector. The lens extends the optical effective active area of the device up to a 5 times larger area than for standard mesa detectors or pixel devices while the electrical active region stays the same. The extended optical area increases the absorption efficiency of the presented device as well as the room temperature performance while it offers a flexible platform for various detector geometries. A photocurrent response increase at room temperature up to a factor of 6 was observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Oxidation Dynamics of Supported Catalytic Cu Clusters: Coupling to Fluxionality

Copper oxide nanoclusters have a wide range of catalytic applications, such as the selective oxidation of hydrocarbons. O 2 binding to the catalyst, activation, and release upon reagent oxidation are key events in these catalytic chemistries. Furthermore, these events are expected to be accompanied by significant structural changes of the Cu clusters, because O atoms integrate into the cluster, rather than bind to its surface. Topping the complexity of the problem, partially oxidized Cu clusters are known to exhibit strong fluxionality and feature diverse and interconverting structures and oxygen contents in conditions of oxidative dehydrogenation (ODH). Hence, a significant dynamic coupling between the “hot” O 2 molecule impacting the cluster at reaction temperatures and the cluster fluxionality can be expected. In this work, we focus on the dynamics of dioxygen integration into a partially oxidized Cu cluster supported on hydroxylated amorphous alumina–a system recently reported to be an exceptionally selective catalyst for cyclohexane ODH with very little CO produced, whose mechanistic underpinnings are of utmost interest. The statistics over a swarm of adsorption and scattering trajectories where O 2 hits various sites on the cluster at reaction temperature shows that the O 2 binding does not only follow the minimal energy paths. O 2 also rarely integrates into the cluster in a single step and instead first binds to a single Cu atom via either an η 1 -O 2 or an η 2 -O 2 mode. Surprisingly, this step often has a higher barrier than the subsequent O 2 integration and dissociation, which in turn take multiple steps and complete the oxidation process. Dynamic trajectories starting from the key transition state of integration of the adsorbed O 2 can also lead to different intermediate structures during or right after the dissociation, due to the energy released from the transition state and the thermal intracluster effects. From these activated O 2 chemisorbed structures, O 2 dissociation occurs with moderate barriers (~0.5 eV), producing multiple final oxidized Cu 4 O 4 states. Hence, a diversity of reaction profiles for the attack of supported Cu cluster by O 2 emerges due to the dynamic effects, with implications for mechanisms, kinetic models, and catalyst design principles.

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

Proton-Coupled Electron Transfer in Molecular Electrocatalysis: Theoretical Methods and Design Principles

Molecular electrocatalysts play an essential role in a wide range of energy conversion processes. The objective of electrocatalyst design is to maximize the turnover frequency and minimize the overpotential for the overall catalytic cycle. Typically the catalytic cycle is dominated by key proton-coupled electron transfer (PCET) processes comprised of sequential or concerted electron transfer and proton transfer steps. A variety of theoretical methods have been developed to investigate the mechanisms, thermodynamics, and kinetics of PCET processes in electrocatalytic cycles. Electronic structure methods can be used to calculate the reduction potentials and pKa’s and to generate thermodynamic schemes, free energy reaction pathways, and Pourbaix diagrams, which indicate the most stable species at each pH and potential. These types of calculations have assisted in identifying the thermodynamically favorable mechanisms under specified experimental conditions, such as acid strength and overpotential. Such calculations have also revealed linear correlations among the thermodynamic properties, which can be used to predict the impact of modifying the ligand, substituents, or metal center. The role of non-innocent ligands, namely ligand protonation or reduction, has also been examined theoretically. In addition, the rate constants for electron and proton transfer reactions, as well as concerted PCET reactions, have been calculated to investigate the kinetics of molecular electrocatalysts. The concerted PCET mechanism is thought to lower the overpotential required for catalysis by avoiding high-energy intermediates. Rate constant calculations have revealed that the concerted mechanism involving intramolecular proton transfer will be favored by designing more flexible ligands that facilitate the proton donor-acceptor motion while also maintaining a sufficiently short equilibrium proton donor-acceptor distance. Overall, theoretical methods have assisted in the interpretation of experimental data and the design of more effective molecular electrocatalysts. The research on the Ni(P2N2)2 catalysts was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

Solis, Brian H.↗
DOE OSTI2020

Magnetic field induced antiferromagnetic cone structure in multiferroic BiFeO 3

Neutron diffraction measurements were performed under high magnetic fields up to 17 T in a multiferroic BiFeO 3 single crystal, in which an intermediate magnetic (IM) phase has been found between the cycloid and canted antiferromagnetic phases [S. Kawachi et al., Phys. Rev. Mater. 1, 024408 (2017)]. We clearly found that the incommensurate magnetic peaks, which split perpendicular to the magnetic field in the cycloid phase, rotate by 90 deg to align parallel to the field in the IM phase. The magnetic structure in the IM phase can be best described by an antiferromagnetic cone (AF cone) structure. The transition from the cycloid to AF cone is of first order and the direction of the magnetic wave vector and the easy plane of the cycloidal component are rotated by 90 deg without changing the cycloidal modulation period, whereas the transition from the AF cone to canted antiferromagnetic phase is gradual and the cone angle becomes smaller gradually without changing the modulation period. Interestingly, the cycloidal component as well as the cone angle in the IM phase shows a large hysteresis between the field increasing and decreasing processes. Finally, this result, combined with the magnetostriction with a large hysteresis previously reported in the IM phase, suggests a strong magnetoelastic coupling.

36 MATERIALS SCIENCE↗
DOE OSTI2011

SCIX IMPACT ON DWPF CPC

A program was conducted to systematically evaluate potential impacts of the proposed Small Column Ion Exchange (SCIX) process on the Defense Waste Processing Facility (DWPF) Chemical Processing Cell (CPC). The program involved a series of interrelated tasks. Past studies of the impact of crystalline silicotitanate (CST) and monosodium titanate (MST) on DWPF were reviewed. Paper studies and material balance calculations were used to establish reasonable bounding levels of CST and MST in sludge. Following the paper studies, Sludge Batch 10 (SB10) simulant was modified to have both bounding and intermediate levels of MST and ground CST. The SCIX flow sheet includes grinding of the CST which is larger than DWPF frit when not ground. Nominal ground CST was not yet available, therefore a similar CST ground previously in Savannah River National Laboratory (SRNL) was used. It was believed that this CST was over ground and that it would bound the impact of nominal CST on sludge slurry properties. Lab-scale simulations of the DWPF CPC were conducted using SB10 simulants with no, intermediate, and bounding levels of CST and MST. Tests included both the Sludge Receipt and Adjustment Tank (SRAT) and Slurry Mix Evaporator (SME) cycles. Simulations were performed at high and low acid stoichiometry. A demonstration of the extended CPC flowsheet was made that included streams from the site interim salt processing operations. A simulation using irradiated CST and MST was also completed. An extensive set of rheological measurements was made to search for potential adverse consequences of CST and MST and slurry rheology in the CPC. The SCIX CPC impact program was conducted in parallel with a program to evaluate the impact of SCIX on the final DWPF glass waste form and on the DWPF melter throughput. The studies must be considered together when evaluating the full impact of SCIX on DWPF. Due to the fact that the alternant flowsheet for DWPF has not been selected, this study did not consider the impact of proposed future alternative DWPF CPC flowsheets. The impact of the SCIX streams on DWPF processing using the selected flowsheet need to be considered as part of the technical baseline studies for coupled processing with the selected flowsheet. In addition, the downstream impact of aluminum dissolution on waste containing CST and MST has not yet been evaluated. The current baseline would not subject CST to the aluminum dissolution process and technical concerns with performing the dissolution with CST have been expressed. Should this option become feasible, the downstream impact should be considered. The main area of concern for DWPF from aluminum dissolution is an impact on rheology. The SCIX project is planning for SRNL to complete MST, CST, and sludge rheology testing to evaluate any expected changes. The impact of ground CST transport and flush water on the DWPF CPC feed tank (and potential need for decanting) has not been defined or studied.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Distributed Energy Resources Customer Adoption Model - Graphical User Interface, Version 2.1.8

The DER-CAM Graphical User Interface has been redesigned to consist of a dynamic tree structure on the left side of the application window to allow users to quickly navigate between different data categories and views. Views can either be tables with model parameters and input data, the optimization results, or a graphical interface to draw circuit topology and visualize investment results. The model parameters and input data consist of tables where values are assigned to specific keys. The aggregation of all model parameters and input data amounts to the data required to build a DER-CAM model, and is passed to the GAMS solver when users initiate the DER-CAM optimization process. Passing data to the GAMS solver relies on the use of a Java server that handles DER-CAM requests, queuing, and results delivery. This component of the DER-CAM GUI can be deployed either locally or remotely, and constitutes an intermediate step between the user data input and manipulation, and the execution of a DER-CAM optimization in the GAMS engine. The results view shows the results of the DER-CAM optimization and distinguishes between a single and a multi-objective process. The single optimization runs the DER-CAM optimization once and presents the results as a combination of summary charts and hourly dispatch profiles. The multi-objective optimization process consists of a sequence of runs initiated by the GUI, including: 1) CO2 minimization, 2) cost minimization, 3) a user defined number of points in-between objectives 1) and 2). The multi-objective results view includes both access to the detailed results of each point generated by the process as well as the generation of a Pareto Frontier graph to illustrate the trade-off between objectives. DER-CAM GUI 2.1.8 also introduces the ability to graphically generate circuit topologies, enabling support to DER-CAM 5.0.0. This feature consists of: 1) The drawing area, where users can manually create nodes and define their properties (e.g. point of common coupling, slack bus, load) and connect them through edges representing either power lines, transformers, or heat pipes, all with user defined characteristics (e.g., length, ampacity, inductance, or heat loss); 2) The tables, which display the user-defined topology in the final numerical form that will be passed to the DER-CAM optimization. Finally, the DER-CAM GUI is also deployed with a database schema that allows users to provide different energy load profiles, solar irradiance profiles, and tariff data, that can be stored locally and later used in any DER-CAM model. However, no real data will be delivered with this version.

Ewald, Friedrich↗
DOE OSTI2021

Improving the accuracy and efficiency of quantum connected moments expansions

The still-maturing noisy intermediate-scale quantum technology faces strict limitations on the algorithms that can be implemented efficiently. In the realm of quantum chemistry, the variational quantum eigensolver (VQE) algorithm has become ubiquitous, with many variations. Alternatively, a promising new avenue has been unraveled by the quantum variants of techniques grounded on expansions of the moments of the Hamiltonian, notably the connected moments expansion (CMX) and the Peeters–Devreese–Soldatov (PDS) energy functional. Common to those approaches is that, upon preparing an approximate ground state used to compute the necessary moments, the accuracy of the estimated ground state energy depends on the degree of overlap between the prepared state and the true ground state. Thus, we use the ADAPT-VQE algorithm to test shallow circuit construction strategies for the purpose of increasing the overlap with the exact ground state, validated by the sizable accuracy improvement herein reported in the PDS and CMX ground state energies. We also show that we can take advantage of the fact that the terms to be measured are highly recurring in different moments, incurring a substantial reduction in the number of necessary measurements. Finally, by coupling this measurement caching with a threshold that determines whether a given term is to be measured based on its associated scalar coefficient, we observe a further reduction in the number of circuit implementations while allowing for tunable accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Nonequilibrium phonon effects in midinfrared quantum cascade lasers

We investigate the effects of nonequilibrium phonon dynamics on the operation of a GaAs-based midinfrared quantum cascade laser over a range of temperatures (77–300 K) via a coupled ensemble Monte Carlo simulation of electron and optical-phonon systems. Nonequilibrium phonon effects are shown to be important below 200 K. At low temperatures, nonequilibrium phonons enhance injection selectivity and efficiency by drastically increasing the rate of interstage electron scattering from the lowest injector state to the next-stage upper lasing level via optical-phonon absorption. As a result, the current density and modal gain at a given field are higher and the threshold current density lower and considerably closer to experiment than results obtained with thermal phonons. By amplifying phonon absorption, nonequilibrium phonons also hinder electron energy relaxation and lead to elevated electronic temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Metrics for quantifying the efficiency of atmospheric CO 2 reduction by marine carbon dioxide removal (mCDR)

Abstract Marine carbon dioxide removal (mCDR) is gaining interest as a tool to meet global climate goals. Because the response of the ocean–atmosphere system to mCDR takes years to centuries, modeling is required to assess the impact of mCDR on atmospheric CO 2 reduction. Here, we use a coupled ocean–atmosphere model to quantify the atmospheric CO 2 reduction in response to a CDR perturbation. We define two metrics to characterize the atmospheric CO 2 response to both instantaneous ocean alkalinity enhancement (OAE) and direct air capture (DAC): the cumulative additionality ( α ) measures the reduction in atmospheric CO 2 relative to the magnitude of the CDR perturbation, while the relative efficiency ( ϵ ) quantifies the cumulative additionality of mCDR relative to that of DAC. For DAC, α is 100% immediately following CDR deployment, but declines to roughly 50% by 100 years post-deployment as the ocean degasses CO 2 in response to the removal of carbon from the atmosphere. For instantaneous OAE, α is zero initially and reaches a maximum of 40%–90% several years to decades later, depending on regional CO 2 equilibration rates and ocean circulation processes. The global mean ϵ approaches 100% after 40 years, showing that instantaneous OAE is nearly as effective as DAC after several decades. However, there are significant geographic variations, with ϵ approaching 100% most rapidly in the low latitudes while ϵ stays well under 100% for decades to centuries near deep and intermediate water formation sites. These metrics provide a quantitative framework for evaluating sequestration timescales and carbon market valuation that can be applied to any mCDR strategy.

Yamamoto, Kana (ORCID:0009000731519234)↗
DOE OSTI2016

Heterologous production of an energy-conserving carbon monoxide dehydrogenase complex in the hyperthermophile Pyrococcus furiosus

In this study, carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus , which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na + /H + antiporter module. This complex oxidizes CO, evolves CO 2 and H 2 , and generates a Na+ motive force that is used to conserve energy by a Na+-dependent ATP synthase. Herein we used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus , which grows optimally at 100° C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H 2 at 80° C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multi-stage heat release of multi-component fuels: Insights and implications for advanced engine operation

Multi-stage heat release (MSHR) is a unique phenomenon typically seen in lean/diluted and low- to intermediate-temperature combustion. Despite its relevance to advanced engine operation, the MSHR of multi-component fuels has barely been quantified. This study aims to characterize the MSHR of multi-component fuels in a rapid compression machine (RCM) at conditions representative of advanced combustion engines. New experimental data are first reported in the RCM at an equivalence ratio of 0.4, pressure of 60 bar and temperatures from 702 to 795 K for a research grade, multi-component gasoline surrogate, termed PACE-20. Here, experiments confirm the existence of MSHR for PACE-20 at all temperatures, and reveal the strong inhibiting effect of temperature on MSHR, where increasing temperature inhibits MSHR by suppressing first stage heat release and promoting second and third stage heat release. A detailed chemical kinetic model is also adopted to model the experiments, with good agreement observed. The response of MSHR characteristics to changes in different engine operating parameters (i.e., temperature, pressure, equivalence ratio and CO 2 dilution level) and fuel compositions (i.e., mole fraction of n-pentane, n-heptane, isooctane, cyclopentane, 1-hexene, ethanol and aromatics in PACE-20) is further evaluated via statistical analysis coupling quasi-random sampling, extensive computer experiments and high-dimensional model representation. The change in MSHR is characterized through 8 quantities of interest (QOIs), i.e., duration and extent of each heat release stage, and their standard deviations. The analysis highlights the dependence of the QOIs on the individual parameters as well as their interplays, with temperature exhibiting the strongest impact among all parameters. Furthermore, it is demonstrated that if MSHR is to be facilitated and combustion phasing is to be extended to enable engine operation at higher compression ratios, it is recommended to operate the engine at low intake temperatures, boosted intake pressures and high CO 2 dilutions (i.e., high EGR levels) with gasoline fuels containing more n-pentane and less aromatics.

42 ENGINEERING↗
DOE OSTI2018

A maximally particle-hole asymmetric spectrum emanating from a semi-Dirac point

Tight binding models have proven an effective means of revealing Dirac (massless) dispersion, flat bands (infinite mass), and intermediate cases such as the semi-Dirac (sD) dispersion. Here, this approach is extended to a three band model that yields, with chosen parameters in a two-band limit, a closed line with maximally asymmetric particle-hole dispersion: infinite mass holes, zero mass particles. The model retains the sD points for a general set of parameters. Adjacent to this limiting case, hole Fermi surfaces are tiny and needle-like. A pair of large electron Fermi surfaces at low doping merge and collapse at half filling to a flat (zero energy) closed contour with infinite mass along the contour and enclosing no carriers on either side, while the hole Fermi surface has shrunk to a point at zero energy, also containing no carriers. The tight binding model is used to study several characteristics of the dispersion and density of states. The model inspired generalization of sD dispersion to a general ±$ \sqrt{k_x^{2n} +k_y^{2m}}$ form, for which analysis reveals that both $n$ and $m$ must be odd to provide a diabolical point with topological character. Evolution of the Hofstadter spectrum of this three band system with interband coupling strength is presented and discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Modeling Oxidative Dehydrogenation of Propane with Supported Vanadia Catalysts Using Multireference Methods

The oxidative dehydrogenation of propane over supported vanadium oxide catalysts poses significant computational challenges due to complex electronic structure changes along the reaction coordinate, driven primarily by changes in the oxidation states of vanadium. To address these challenges, we systematically test quantum chemical methods, including multireference (MR) approaches, domain-based local pair natural orbital coupled cluster theory (DLPNO-CCSD(T)), and density functional theory (DFT). The initial C–H bond-breaking transition state requires MR treatment due to its multireference character, while subsequent steps permit efficient single-reference calculations. For the rate-limiting C–H activation step mediated by the vanadyl moiety, complete 1 active space second-order perturbation theory (CASPT2) yields an apparent activation barrier (E app 600K ) of 138 kJ/mol, consistent with experimental values (134 ± 4 kJ/mol; Gruene et al. Catal. Today 2010, 157, 137). In contrast, DLPNO-CCSD(T) overestimates this barrier (198 kJ/mol), whereas DFT predictions span 125–150 kJ/mol, depending on the functional. Our multireference investigation of this transition metal oxide-catalyzed process demonstrates that an active space that incorporates the C–H σ and V=O σ/π bonding orbitals, oxygen lone pairs, and their antibonding counterparts adequately captures electronic structure changes along the chemical transformation. Furthermore, these findings provide a general strategy for active space selection in transition metal oxide-catalyzed C/O–H bond activation reactions. The reference dataset from this work, which includes MR calculations with manually selected active spaces for all intermediates and transition states in the propane ODH reaction network, will serve as a benchmark for automating active space selection in similar systems.

Catalysts↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Excitable dynamics in high-Lewis number premixed gas combustion at normal and microgravity

Freely-propagating, premixed gas flames in high-Lewis (Le) number, quiescent mixtures are studied experimentally in tubes of various diameter at normal (lg) and microgravity (mu g). A premixture of lean butane and oxygen diluted with helium, argon, neon, nitrogen or a mixture of multiple diluents is examined such that the thermal diffusivity of the mixture (and to a lesser extent, the mass diffusivity of the rate-limiting component) is systematically varied. In effect, different diluents allow variation of the Le without changing the chemistry. The flames are recorded with high speed cinematography and their stability is visually assessed. Different modes of propagation were observed depending on the diameter of the tubes (different conductive heat loss), the composition of the mixture and the g-level. At 1g, four modes of propagation were observed in small and intermediate diameter tubes (large conductive heat loss): (1) steadily propagating flames, (2) radial and longitudinal pulsating flames, (3) 'wavering' flames, and (4) rotating spiral flames. As the diameter of the tube increases, the radial modes become more pronounced while the longitudinal modes systematically disappear. Also, multiple, simultaneous, spatially-separated 'pacemaker' sites are observed in intermediate and large diameter tubes. Each site starts as a small region of high luminosity and develops into a flamelet which assumes the form of one of the fore mentioned modes. These flamelets eventually interact, annihilate each other in their regions of intersection and merge at their newly created free-ends. For very large tubes, radially-propagating wave-trains (believed to be 'trigger waves') are observed. These are analogous to the radial pulsations observed in the smaller diameter tubes. At mu g, three modes of propagation have been observed: (1) steadily propagating flames, (2) radial and longitudinal pulsating flames, and (3) multi-armed, rotating flames. Since the pulsating mode exists at mu g and 1g, buoyant flicker is not the mechanism which drives the pulsations. Moreover, all of the instabilities at 1g and mu g have characteristic frequencies on the O(100Hz). This value is lower than the fundamental, longitudinal acoustic frequencies of the tubes which suggests that the instabilities are not acoustically driven. The patterns formed by this reaction bear remarkable similarities with the patterns formed in most excitable media when the behavior of the system is driven by couplings between chemical reaction and diffusion (e.g., Belousov-Zhabotinsky reaction, Patterns in slime molds, spiral waves in the retina of a bird's eye). While it is recognized that the chemical mechanism associated with this premixed gas reaction is exponentially sensitive to temperature and undoubtedly different from those which govern previously observed excitable media (most are isothermal, or weakly exothermic, liquid phase reactions), similar spatial and temporal patterns should not come as a complete surprise considering heat and mass diffusion are self similar. It is concluded that this premixed gas system is a definitive example of a diffusive-thermal, gas-phase oscillator based on these experimental results and their favorable comparison with theory.

Pearlman, Howard↗