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At least 739 records · Page 41

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C $\bar{β}$ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deciphering the Conflict Between Ion and Electron Percolating Networks in Solid-State Battery Cathodes

High-energy- and power-density solid state batteries require an optimal cathode composition and microstructural arrangement of cathode active material, solid-state electrolyte, conductive carbon, and binder to simultaneously support lithium-ion transport, electron conduction, and storage capacity. The ion and electron conducting phases in solid-state cathodes counteract each other's percolating networks as their mass ratios increase or decrease relative to each other. Here, we investigate targeted mass ratio variations of argyrodite solid electrolyte and two different types of conductive carbon (particles and fibers) in composite LiNi0.8Mn0.1Co0.1O2 (NMC811) solid-state cathodes to ascertain the ionic-electronic tradeoffs in cathode performance. Through ionic and electronic conductivity measurements on composite cathodes, as well as rate-testing and cycling performance in full cells, it is shown that the conductive carbon fibers form a percolative electronic network within the composite at a lower mass ratio (3-5 wt%) than particulate carbon (>5 wt%). The threshold to achieve electronic percolation coincides with higher accessible capacity in the cathode as the active material particles become electronically connected. However, carbon loadings beyond this percolation threshold lead to increased ion transport resistance, arising from disruptions to ionic conduction pathways and degraded contact at the interface between the electrolyte and active materials. Imaging, spectroscopy, and physics-based models quantitatively describe the relationship between carbon and electrolyte compositions and the cell's capacity and rate performance through percolation theory. This work demonstrates the importance of quantitatively understanding percolating networks in solid-state cells and that strategic engineering of conductive carbon morphologies can further increase the energy- and power-density of solid-state cells.

25 ENERGY STORAGE↗

Temperature Knowledge and Model Correlation for the Soil Moisture Active and Passive (SMAP) Reflector Mesh

NASA's Earth observing Soil Moisture Active & Passive (SMAP) Mission is scheduled to launch in November 2014 into a 685 km near-polar, sun synchronous orbit. SMAP will provide comprehensive global mapping measurements of soil moisture and freeze/thaw state in order to enhance understanding of the processes that link the water, energy, and carbon cycles. The primary objectives of SMAP are to improve worldwide weather and flood forecasting, enhance climate prediction, and refine drought and agriculture monitoring during its 3 year mission. The SMAP instrument architecture incorporates an L-band radar and an L-band radiometer which share a common feed horn and parabolic mesh reflector. The instrument rotates about the nadir axis at approximately 15 rpm, thereby providing a conically scanning wide swath antenna beam that is capable of achieving global coverage within 3 days. In order to make the necessary precise surface emission measurements from space, a temperature knowledge of 60 deg C for the mesh reflector is required. In order to show compliance, a thermal vacuum test was conducted using a portable solar simulator to illuminate a non flight, but flight-like test article through the quartz window of the vacuum chamber. The molybdenum wire of the antenna mesh is too fine to accommodate thermal sensors for direct temperature measurements. Instead, the mesh temperature was inferred from resistance measurements made during the test. The test article was rotated to five separate angles between 10 deg and 90 deg via chamber breaks to simulate the maximum expected on-orbit solar loading during the mission. The resistance measurements were converted to temperature via a resistance versus temperature calibration plot that was constructed from data collected in a separate calibration test. A simple thermal model of two different representations of the mesh (plate and torus) was created to correlate the mesh temperature predictions to within 60 deg C. The on-orbit mesh temperature will be predicted using the correlated analytical thermal model since direct measurements from in-situ flight thermal sensors are not possible.

Mikhaylov, Rebecca↗

Electronic structure prediction of medium and high entropy alloys across composition space

We propose machine learning (ML) models to predict the electron density — the fundamental unknown of a material’s ground state — across the composition space of concentrated alloys. From this, other physical properties can be inferred, enabling accelerated exploration. A significant challenge is that the number of descriptors and sampled compositions required for accurate prediction grows rapidly with species. To address this, we employ Bayesian Active Learning (AL), which minimizes training data requirements by leveraging uncertainty quantification capabilities of Bayesian Neural Networks. Compared to the strategic tessellation of the composition space, Bayesian-AL reduces the number of training data points by a factor of 2.5 for ternary (SiGeSn) and 1.7 for quaternary (CrFeCoNi) systems. We also introduce easy-to-optimize, body-attached-frame descriptors, which respect physical symmetries while keeping descriptor-vector size nearly constant as alloy complexity increases. Our ML models demonstrate high accuracy and generalizability in predicting both electron density and energy across composition space.

materials science↗

Active Flutter Suppression Using Reduced-Order Modeling for Transonic Aeroservoelastic Control Law Development

In this paper, several aerodynamic reduced-order models (ROMs) are generated and coupled with structural models to form aeroelastic ROMs. The aerodynamic ROMs generated here include the effects of control surface motion and are appropriate for use in aeroservoelastic applications. Simple observer-based full-state feedback controllers were designed from these aeroelastic ROMs. Additionally, observer gain matrices were designed from and coupled to the aeroelastic ROMs. Each (linear) observer was then used to estimate the dynamics of a (nonlinear) stand-alone computational fluid-structure dynamics simulation. Then, using the estimated states and the full-state feedback controller, control surface commands were fed back into the computational fluid-structure dynamics simulation to successfully achieve active flutter suppression. The process, as well as some results, are presented in this paper.

Waite, Josiah M.↗

Simulating Extreme Precipitation in the United States in the Energy Exascale Earth System Model: Investigating the Importance of Representing Convective Intensity versus Dynamic Structure (Final Report)

Weather events that produce extreme precipitation are associated with severe flooding and winds that result in thousands of deaths and billions of dollars in damages annually in the United States (U.S.). This project aims to improve understanding of the small- and large-scale processes that govern these events and improve our ability to project changes in these extreme events under the influences of natural variability and human activities. We focus on two promising directions in the development of the U.S. Department of Energy’s Energy Exascale Earth System Model (E3SM) to investigate the tradeoffs between resolving the convective-scale processes that control the intensity versus the intermediate-scale processes that control the dynamic structure of the most prominent extreme precipitation events that impact the U.S. throughout the year (i.e., mesoscale convective systems, tropical cyclones, and extratropical cyclone).

58 GEOSCIENCES↗

Enhanced active-sterile neutrino polarizability at the intensity frontier

Electromagnetic probes of neutrinos can provide insights into physics beyond the Standard Model. Among the possible electromagnetic interactions of neutrinos is neutrino polarizability, a dimension-7 effective operator that couples two neutrinos to two photons. In this manuscript, we study a realization of the neutrino polarizability operator in which one of the active neutrinos is replaced by a sterile neutrino. We derive new constraints on this active-sterile neutrino polarizability from its contribution to neutrino-nucleus scattering with a single photon in the final state at neutrino experiments. We show that a realization of this operator via a light mediator can explain the MiniBooNE low-energy excess while remaining consistent with other experimental constraints. Finally, we comment on additional model realizations of this higher-dimensional operator.

Neutrinos↗

Implementation of active sites to capture pitting of oxidizing carbon materials in DSMC.

In this work we demonstrate a newly developed capability to capture pitting of carbon fibers in DSMC simulations, specifically using the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code [1]. State-of-the-art reactive surface models in DSMC compute collision dependent carbon consumption rates (usually through desorption of CO) based on a set of surface reactions that has been derived from molecular beam experiments [2]. The reactivity on each carbon surface element is constant in those models, such that the carbon surface recedes uniformly as a result of ablation. However, it is well known that in reality the carbon surface has locally different reaction rates due to the presence of defects at the atomic scale [3]. These defective sites have a much higher reactivity than the average sites (2-3 orders of magnitude) and are first to react during ablation leading to its removal. This causes all the neighboring atoms to be defective and increase their reactivity, thus leading to the localized carbon removal around these ”active” sites (as shown in Fig. 1). In this manner, these highly reactive defective sites serve as nucleation sites for the formation and growth of etch pits with potentially detrimental effects on the structural integrity. Recently a detailed surface chemistry framework was developed in SPARTA, capable of incorporating various reaction mechanisms such as adsorption, desorption, Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms [4]. Within this framework, we have implemented the capability of a single surface having multiple site sets with different reactivities. Using this feature, we can simulate the presence of active sites on carbon surfaces, whose reactivity is much greater than an average site as a result of defects. We have implemented the active site fraction as a property of surface elements within SPARTA, which is directly proportional to the local reactivity of each surface element. By introducing an initial distribution of the active site fraction across the carbon surface, and propagating it in a manner that mimics the evolution of real reacting carbon surfaces, we are able to capture the formation and growth of etch pits as a result of surface consumption reactions such as oxidation.

DSMC↗

Simplified calculation of the area specific impedance for solid-state battery design

Simplified algebraic area specific impedance (ASI) correlations have been developed for solid-state composite battery electrodes made of a single ion conducting electrolyte, conductive additive, and intercalation active material. Two ASI expressions were developed, one for short times ( i.e. , pulsed power operation) and another for the pseudo steady state operation (i.e., sustained discharge for energy estimation). A full electrochemical model based on porous electrode theory was developed to examine the accuracy of the simplified ASI expressions. The simplified expressions agree favorably with full model results over a wide range of parameters (i.e. , electrode thicknesses, electrolyte conductivities, solid-state diffusion coefficients, specific surface areas, etc.) and conditions (i.e. , C-rates, states of charge, and pulse times). Under most conditions, the error between the full model and the correlations is well below 7 %. Higher errors were observed for the pseudo steady state expression at high/ low states of charge where the assumption of uniform reaction distributions loses validity. Here, the short time ASI has higher error at low states of charge due to the nonlinearity of the open circuit voltage equation, which is assumed linear in the formulation of the simplified algebraic expression.

25 ENERGY STORAGE↗

GHB analogs confer neuroprotection through specific interaction with the CaMKIIα hub domain

Ca 2+ /calmodulin-dependent protein kinase II alpha subunit (CaMKIIα) is a key neuronal signaling protein and an emerging drug target. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers, yet pharmacological modulation of the hub domain has never been demonstrated. Here, using a combination of photoaffinity labeling and chemical proteomics, we show that compounds related to the natural substance γ-hydroxybutyrate (GHB) bind selectively to CaMKIIα. By means of a 2.2-Å x-ray crystal structure of ligand-bound CaMKIIα hub, we reveal the molecular details of the binding site deep within the hub. Furthermore, we show that binding of GHB and related analogs to this site promotes concentration-dependent increases in hub thermal stability believed to alter holoenzyme functionality. Selectively under states of pathological CaMKIIα activation, hub ligands provide a significant and sustained neuroprotection, which is both time and dose dependent. This is demonstrated in neurons exposed to excitotoxicity and in a mouse model of cerebral ischemia with the selective GHB analog, HOCPCA (3-hydroxycyclopent-1-enecarboxylic acid). Together, our results indicate a hitherto unknown mechanism for neuroprotection by a highly specific and unforeseen interaction between the CaMKIIα hub domain and small molecule brain-penetrant GHB analogs. This establishes GHB analogs as powerful tools for investigating CaMKII neuropharmacology in general and as potential therapeutic compounds for cerebral ischemia in particular.

59 BASIC BIOLOGICAL SCIENCES↗

Considerations for AMI-Based Operations for Distribution Feeders

More than $5 billion in investments in advanced metering infrastructure (AMI) technologies, AMI deployments, as pervasive secondary network voltage monitoring systems, provide opportunities for utility operations and controls. This paper focuses on the considerations for AMI-based tools and techniques as the industry moves toward operationalizing such large data sets. Phase identification is a first such tool. Numerous distribution network analysis, monitoring, and control applications - including volt/volt-ampere reactive control, state estimation, and distribution automation - require accurate phase connectivity information in the system models. The phase connectivity database maintained by utilities is inaccurate because of a significant amount of missing data, restoration activities, and network reconfiguration. Existing phase identification techniques that estimate phase connectivity work well in distribution feeders that have low or no photovoltaic (PV) generation; however, they fail to identify the phases accurately when considerable PV generation is present. This work addresses the phase identification problem in the presence of high PV generation using statistical analysis methods. Further, insights into the AMI data requirements for this application in terms of data window length and resolution are provided using sensitivity analysis performed on an actual distribution feeder model of San Diego Gas & Electric Company. The results of this study show that the phase connectivity, even in the presence of high PV generation, can be accurately identified using statistical analysis of AMI data of 1 day.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Comparison of Eulerian Bin and Lagrangian Particle-Based Schemes in Simulations of Pi Chamber Dynamics and Microphysics

This paper presents a comparison of simulations applying either a traditional Eulerian bin microphysics or a novel particle-based Lagrangian approach to represent CCN activation and cloud droplet growth. The Eulerian microphysics solve the evolution equation for the spectral density function, whereas the Lagrangian approach follows computational particles referred to as superdroplets. Each superdroplet represents a multiplicity of natural droplets that makes the Lagrangian approach computationally feasible. The two schemes apply identical representation of CCN activation and use the same droplet growth equation; these make direct comparison between the two schemes practical. The comparison, the first of its kind, applies an idealized simulation setup motivated by laboratory experiments with the Pi Chamber and previous model simulations of the Pi Chamber dynamics and microphysics. The Pi Chamber laboratory apparatus considers interactions between turbulence, CCN activation, and cloud droplet growth in moist Rayleigh–Bénard convection. Simulated steady-state droplet spectra averaged over the entire chamber are similar, with the mean droplet concentration, mean radius, and spectral width close in Eulerian and Lagrangian simulations. Small differences that do exist are explained by the inherent differences between the two schemes and their numerical implementation. The local droplet spectra differ substantially, again in agreement with the inherent limitations of the theoretical foundation behind each approach. There is a general agreement between simulations and Pi Chamber observations, with simplifications of the CCN activation and droplet growth equation used in the simulations likely explaining specific differences.

54 ENVIRONMENTAL SCIENCES↗

Griffin/Pronghorn PBMR-400 Benchmark Results [Slides]

Content Overview: 1) Pronghorn & Griffin, MOOSE based applications overview: Codes capabilities description & MOOSE ecosystem overiew; Current research activities and synergies with other projects; Different multiphysics coupling scheme description. 2) PBMR-400 Benchmark: OECD NEA Benchmark and Pronghorn/Griffin models description; Standalone NK Ex1 and TH Ex2 Results description; Coupled Steady state Ex3; Results analysis for Transiet Ex4a (100-40-100 Load Following) & Ex3 (Protected PLOFC). 3) Conclusions $ Future steps.

97 MATHEMATICS AND COMPUTING↗

Water foraging with dynamic roots in E3SM; The role of roots in terrestrial ecosystem memory on intermediate timescales (Final Technical Report)

Terrestrial ecosystems can show sustained responses to stress events that may last for years after the initial perturbation. This phenomenon is referred to as legacy or memory and it emerges from a set of ecosystem processes that are poorly captured by Earth System and Land Surface Models. Consequently, these models struggle to predict the impact that extreme climate events have on surface energy, carbon and hydrological exchange once a stressor such as drought has relaxed or in response to repeated exposure to stress. In this project, we set out to test how the addition of dynamic root profiles in land surface models impact the capacity for Earth System Models, such as the Department of Energy’s E3SM, to capture realistic legacy effects. Observations have shown that vegetation shifts their root profiles during stress events to forage for water and these altered root profiles may take years to relax back to the initial state. We hypothesized that the alteration of the belowground root structures may be a source of terrestrial ecosystem legacy that is missing from models. To test this idea we undertook three core activities. (1) We developed a global-scale analysis of the impact of dynamic roots on ecosystem legacy building from a recently developed dynamic root module. (2) We developed new root dynamics in the DOE’s Energy Land Model (ELM) that allowed not only root profiles to shift their profile but also simultaneously alter carbon allocation to fine root pools. We then tested the impact of these new dynamics with intensive sensitivity analysis at four long-term AmeriFlux sites. (3) We undertook detailed isotopic analysis of tree rings from these AmeriFlux sites to assess ecophysiological and ecohydrological legacy to stress events that can be used to benchmark the sensitivity experiments with ELM. From these core activities, we report the following key findings. Firstly, on a global scale, the addition of dynamic roots led to chronically water-stressed ecosystems recovering faster to climate stress while wetter ecosystem showed enhanced legacy. This is because across ecosystems, stress events were almost universally associated with water shortages that led to the development of deeper root profiles. These deeper root profiles proved beneficial for recovery from drought stress. While the root dynamics did not universally improve the modeled representation of legacy it showed complex transient dynamics that emerge from the addition of dynamic roots. Secondly, the sensitivity analysis illustrated long term shifts in rooting depths away from the prescribed default profile suggesting that initializing of root profiles could benefit from spin-up simulations that converge on locally optimized root profiles. In addition, by enabling dynamic allocation some of the sites predicted unrealistically low allocation to roots (and high allocation to leaves). While these changes did not dramatically alter modeled gross primary productivity, they illustrated that without more sophisticated root processes in models, there is little penalty to dramatically disinvest in roots. Thirdly, the isotopic analysis of tree rings showed highly distinct legacy responses across species and sites. For example, T. canadensis showed reduced transpiration the year after stress events illustrated by sustained elevated $\delta^{18}$O. In contrast, A saccharum displayed elevated $\delta^{13}$C associated with reduced stomatal conductance in response to the previous years’ stress event. These geochemical signatures of legacy were present despite tree growth returning to normal the year after the stress. The results show the importance of species-level dynamics in legacy that are absent in modeling that assumes common traits within plant functional types. In summary, the work here established new avenues to explore root dynamics in models while illustrating how additional root processes are needed before dynamic carbon allocation can be implemented. Lastly, this project provided mentorship to a postdoctoral fellow, training for an early career scientist and multiple undergraduate students recruited from a minority serving institution.

54 ENVIRONMENTAL SCIENCES↗

The GSFC NASTRAN thermal analyzer new capabilities

An overview of four analysis capabilities, which developed and integrated into the NASTRAN Thermal Analyzer, is given. To broaden the scope of applications, these additions provide the NTA users with the following capabilities: (1) simulating a thermal louver as a means of the passive thermal control, (2) simulating a fluid loop for transporting energy as a means of the active thermal control, (3) condensing a large sized finite element model for an efficient transient thermal analysis, and (4) entering multiple boundary condition sets in a single submission for execution in steady state thermal analyses.

Lee, H. P.↗

Instability of non-zonal baroclinic flows

Linear instabilities have been found for tropospheric flows consisting of a mean zonal component and a tilted, forced, stationary wave. The eigensolutions of maximum growth rate provide an adequate explanation of the location and structure of regions of maximum bandpass transient activity (storm tracks). The study also highlights the importance of adequate resolution in models involving first-order coupling mechanisms, such as a standing wave. It identifies the curvature of the mean state as a possibly significant factor in determining the 'baroclinicity' of a region.

Niehaus, M. C. W.↗

Photovoltaic concentrator pointing dynamics and plasma interaction study

The objectives of this experiment are to use the Space Technology Experiments Platform (STEP) system to demonstrate the viability of concentrator photovoltaic arrays by: (1) configuring a deployable mast on the STEP pallet with concentrator mass models and some active photovoltaic modules; (2) measuring the array pointing dynamics under normal rotation as well as disturbance conditions; (3) performing an array plasma interaction experiment to determine the steady-state plasma losses under various voltage conditions; and (4) providing active distributed control of the support truss to determine the improvement in dynamic response. Experiment approach and test control and instrumentation are described.

Stern, T. G.↗

High Temperature Superconductivity in Praseodymium Doped (0%, 2%, 4%) in Melt-Textured Y(1-x)Pr(x)Ba2Cu3O(7-delta) Systems

A study of the magnetic and structural properties of the alloy Y(1-x)Pr(x)Ba2Cu3O(7-delta) of 0%, 2%, and 4% doping of praseodymium is presented. The resulting oxides of the alloy series are a high-temperature superconductor Y-Ba-Cu-O, which has an orthorhombic superconducting crystal-lattice. Magnetic relaxation studies have been performed on the Y-Pr-Ba-CuO bulk samples for field orientation parallel to the c-axis, using a vibrating sample magnetometer. Relaxation was measured at several temperatures to obtain the irreversible magnetization curves used for the Bean model. Magnetization current densities were derived from the relaxation data. Field and temperature dependence of the logarithmic flux-creep relaxation was measured in critical state. The data indicates that the effective activation energy U(eff) increases with increasing T between 77 K and 86 K. Also, the data shows that U(eff)(T) and superconducting transition temperature, Tc, decreased as the lattice parameters increased with increasing Pr ion concentration, x, for the corresponding Y(1-x)Pr(x)Ba(x)Cu3O(7-delta) oxides. One contribution to Tc decrease in this sampling is suspected to be due to the larger ionic radius of the Pr(3+) ion. The upper critical field (H(sub c2)) was measured in the presence of magnetic field parallel to the c axis. A linear temperature dependence with H(sub c2) was obtained.

James, Claudell↗