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Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site
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Investigation of Farm-to-Farm Interactions and Blockage Effects from AWAKEN using Large-Scale Numerical Simulations
A large-scale numerical computation of five wind farms was performed as a part of the American Wake Experiment (AWAKEN). This high-fidelity computation used the ExaWind/AMR-Wind LES solver to simulate a 100km × 100km domain containing 541 turbines under unstable atmospheric conditions matching previous measurements. The turbines were represented by Joukowski and OpenFAST coupled actuator disk models. Results of this qualitative comparison illustrate the interactions with wind farms with large scale ABL structures in the flow, as well as the extent of downstream wake penetration in the flow and blockage effects around wind farms.
Investigation of Theoretical Solutions to a Bottom-Raised Oscillating Surge Wave Energy Converter (OSWEC) Through Experimental and Parametric Studies
Experiments were conducted on a wave tank model of a bottom raised oscillating surge wave energy converter (OSWEC) model in regular waves. The OSWEC model shape was a thin rectangular flap, which was allowed to pitch in response to incident waves about a hinge located at the intersection of the flap and the top of the supporting foundation. Torsion springs were added to the hinge in order to position the pitch natural frequency at the center of the wave frequency range of the wave maker. The flap motion as well as the loads at the base of the foundation were measured. The OSWEC was modeled analytically using elliptic functions in order to obtain closed form expressions for added mass and radiation damping coefficients, along with the excitation force and torque. These formulations were derived and reported in a previous publication by the authors. While analytical predictions of the foundation loads agree very well with experiments, large discrepancies are seen in the pitch response close to resonance. These differences are analyzed by conducting a sensitivity study, in which system parameters, including damping and added mass values, are varied. The likely contributors to the differences between predictions and experiments are attributed to tank reflections, standing waves that can occur in long, narrow wave tanks, as well as the thin plate assumption employed in the analytical approach.
Combined Experimental and Theoretical Investigations of n-Type BiFeO 3 for Use as a Photoanode in a Photoelectrochemical Cell
Combined experimental and theoretical investigations were performed to evaluate the potential of n-type BiFeO 3 as a photoanode. While previous experimental and theoretical studies on BiFeO 3 mainly focused on its ferroelectric properties, several studies have reported the advantages of BiFeO 3 as a photoelectrode for solar water splitting (e.g. bandgap energy and band edge positions relative to water reduction and oxidation potentials). However, the photoelectrochemical properties of n-type BiFeO 3 have not yet been thoroughly investigated. In our experimental investigation, we developed an electrodeposition-based synthesis to prepare uniform n-type BiFeO 3 thin-film electrodes. Furthermore, using a heat treatment under a N 2 environment, we intentionally introduced additional oxygen vacancies into the pristine n-type BiFeO 3 electrodes to increase the majority carrier density. The bandgaps, flatband potentials, photocurrent onset potentials, photocurrent generation, and photoelectrochemical stabilities of the pristine and N 2 -treated BiFeO 3 photoanodes were investigated comparatively to improve our understanding of BiFeO 3 photoanodes and to examine the effect of oxygen vacancies on the photoelectrochemical properties of BiFeO 3 . In our theoretical investigation, we performed first-principles calculations and demonstrated the formation of a small polaron when an extra electron was introduced into the BiFeO 3 lattice. Changes in electronic states cause by the small polaron formation were carefully investigated. We also examined the effects of oxygen vacancies on electron polaron formation and carrier concentration in BiFeO 3 . Using charge formation energy calculations and referencing charge transition levels to the free electron polaron level instead of to the conduction band minimum, we showed that the oxygen vacancy is capable of serving as a donor to enhance the carrier concentration of BiFeO 3 . Furthermore, our theoretical results agree well with our experimental findings. Together, the new experimental and theoretical results and discussion provided in this study have considerably improved our understanding of n-type BiFeO 3 as a photoanode.
Investigations of Polymethacrylate Tribochemical Films Using X-Ray Spectroscopy and Optical Profilometry
This study investigates the elemental composition and surface morphology of solid tribochemical films formed on steel surfaces. The reversible addition-fragmentation chain transfer (RAFT) method was used to synthesize nine different metal-free polymers, which were blended into commercial base oils. The polymers were either homopolymers of dodecyl methacrylate and ethylhexyl methacrylate or were co-polymers of these monomers with six polar monomers. After tribological testing at 100 degrees C using the ball-on-flat geometry, the resulting tribochemical films were imaged using scanning electron microscopy (SEM) and optical microscopy. The resulting tribochemical films have thicknesses around 50-100 nm. Two of the films corresponding to small (P1-imidazole-containing copolymer) and large (P3-less polar homopolymer) wear were cross-sectioned using focused ion beam (FIB) and analyzed for elemental composition using energy-dispersive X-Ray (EDX) mapping. Oxygen and nitrogen enrichment was observed, consistent with the relative chemical composition of the precursor polymers. Transmission electron microscopy (TEM) evidence suggests that at the worn surface, some organic elements penetrate or are mixed into the steel substrate giving an interlocking appearance. The two samples examined with TEM showed that P1 tribofilm is diffused or mixed with the steel substrate more so than P3, suggesting a stronger affinity and contact during tribofilm formation.
Ab-Initio Investigation of Finite Size Effects in Rutile Titania Nanoparticles with Semilocal and Nonlocal Density Functionals
In this work, we employ hybrid and generalized gradient approximation (GGA) level density functional theory (DFT) calculations to investigate the convergence of surface properties and electronic gap of rutile titania nanoparticles with particle size. The surface energies and electronic gaps are calculated for cuboidal particles with minimum dimension ranging from 3.7 Angstrom (24 atoms) to 10.3 Angstrom (384 atoms) using a highly-parallel real-space DFT code to enable hybrid level DFT calculations of larger nanoparticles than are typically practical. We deconvolute the geometric and electronic finite size effects in surface energy, and evaluate the influence of defects on electronic gap and density of states (DOS). The electronic finite size effects in surface energy vanish when the minimum length scale of the nanoparticles becomes greater than 10 Angstrom. We show that this length scale is consistent with a computationally efficient numerical analysis of the characteristic length scale of electronic interactions. The surface energy of nanoparticles having minimum dimension beyond this characteristic length can be approximated using slab calculations that account for the geometric defects. In contrast, the finite size effects on the electronic gap and DOS is highly dependent on the shape and size of these particles. Furthermore, the DOS for cuboidal particles and more realistic particles constructed using the Wulff algorithm reveal that defect states within the electronic gap play a key role in determining the eigen value distribution of nanoparticles and the electronic gap does not converge to the bulk limit for the particle sizes investigated.
LiDAR Measurements to Investigate Farm-to-Farm Interactions at the AWAKEN Experiment
The exponential growth of wind energy and the need to exploit wind resources over areas with higher energy potential have led to the construction of neighboring wind turbines and farms with relatively small separation distances. As a result, for specific wind and atmospheric conditions, the wakes generated by an upstream wind farm may affect wind resources available for a downstream wind farm resulting in detrimental impacts on energy harvesting and structural loads for the downwind wind turbines. Distances between neighboring wind farms are typically larger than those associated with intra-wind-farm wake interactions, generating cumulative wakes whose characteristics might differ from those predicted through classical engineering wake models. These phenomena are referred to as farm-to-farm interactions. A better understanding and characterization of farm-to-farm interactions is one of the science goals tackled by the ongoing American WAKE experimeNt (AWAKEN). The site under investigation for this field campaign comprises two large wind farms in northern Oklahoma, USA, which are spaced roughly 5km apart along the prevailing South-North wind direction. To investigate possible interactions between these two wind farms, the WindFluX mobile LiDAR station has been deployed mainly to perform volumetric scans over their gap region. In this paper, preliminary results from these LiDAR volumetric scans will be discussed, specifically for a case with multiple wind turbine wakes evolving during the occurrence of a low-level jet.
Symmetry-mode analysis for local structure investigations using pair distribution function data
Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.
Investigating anode off-gas under spark-ignition combustion for SOFC-ICE hybrid systems
Solid oxide fuel cell – internal combustion engine (SOFC-ICE) hybrid systems are an attractive solution for electricity generation. The system can achieve up to 70% theoretical electric power conversion efficiency through energy cascading enabled by utilizing the anode off-gas from the SOFC as the fuel source for the ICE. Experimental investigations were conducted with a single cylinder Cooperative Fuel Research (CFR) engine by altering fuel-air equivalence ratio (φ), and compression ratio (CR) to study the engine load, combustion characteristics, and emissions levels of dry SOFC anode off-gas consisting of 33.9% H 2 , 15.6% CO, and 50.5% CO 2 . The combustion efficiency of the anode off-gas was directly evaluated by measuring the engine-out CO emissions. The highest net-indicated fuel conversion efficiency of 31.3% occurred at φ = 0.90 and CR = 13:1. These results demonstrate that the anode off-gas can be successfully oxidized using a spark ignition combustion mode. The fuel conversion efficiency of the anode tail gas is expected to further increase in a more modern engine architecture that can achieve increased burn rates in comparison to the CFR engine. NO x emissions from the combustion of anode off-gas were minimal as the cylinder peak temperatures never exceeded 1800 K. This experimental study ultimately demonstrates the viability of an ICE to operate using an anode off-gas, thus creating a complementary role for an ICE to be paired with a SOFC in a hybrid power generation plant.
Rheology Investigations with Sludges from Metro Vancouver
Rheological investigation were performed with primary and secondary waste water treatment sludge. Using a rheometer equipped with a high pressure/temperature cell, flow curves were generated over shear rate at 0 to 1000 s-1. Temperature sweeps spanning 25 to 300 C were also performed are are reported here. The original release, PNNL-SA-185826, is being revised. The revision include a revision table, a disclaimer, and the underlying data set is being added.
It takes a village: using a crowdsourced approach to investigate organic matter composition in global rivers through the lens of ecological theory
Though community-based scientific approaches are becoming more common, many scientific efforts are conducted by small groups of researchers that together develop a concept, analyze data, and interpret results that ultimately translate into a publication. Here, we present a community effort that breaks these traditional boundaries of the publication process by engaging the scientific community from initial hypothesis generation to final publication. We leverage community-generated data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to study organic matter composition through the lens of ecological theory. This community endeavor will use a suite of paired physical and chemical datasets collected from 97 river corridors across the globe. With our first step aimed at ideation, we engaged a community of scientists from 20 countries and 60 institutions, spanning disciplines and career stages by holding a virtual workshop (April 2021). In the workshop, participants generated content for questions, hypotheses, and proposed analyses based on the WHONDRS dataset. These ideation efforts resulted in several narratives investigating different questions led by different teams, which will be the basis for research articles in a Frontiers in Water collection. Currently, the community is collectively analyzing, interpreting, and synthesizing these data that will result in seven crowdsourced articles using a single, existing WHONDRS dataset. The use of a shared dataset across articles not only lowers barriers for broad participation by not requiring generation of new data, but also provides unique opportunities for emergent learning by connecting outcomes across studies. Here we will explain methods used to enable this community endeavor aimed to promote a greater diversity of thinking on river corridor biogeochemistry through community science.
Investigation of Sr[subscript 0.7]Ca[subscript 0.3]FeO[subscript 3] Oxygen Carriers with Variable Co
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Investigating corrosion behavior of Ni and Ni-20Cr in molten ZnCl2
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Investigation of relaxation behavior in highly rejuvenated bulk metallic glasses by in-situ synchrotron X-ray scattering
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Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface
Mercury (Hg) pollution is a global environmental problem, but many key transformations among 29 various Hg species are not well understood. Although anaerobic microorganisms are the primary 30 producers of monomethylmercury (MMeHg), the abiotic formation of dimethylmercury (DMeHg) 31 from MMeHg have been suggested to account for a large portion of DMeHg in the ocean. It has 32 been shown that abiotic formation of DMeHg from MMeHg can be facilitated by reduced sulfur 33 groups on mineral surfaces. However, a detailed mechanistic understanding of this reaction is 34 lacking. Here we perform density functional theory (DFT) calculations to explore mechanisms of 35 DMeHg formation on the 110 surface of a CdS(s) (hawleyite) nanoparticle. We show that 36 coordination of MMeHg substituents to adjacent reduced sulfur groups protruding from the surface 37 facilitate DMeHg formation and that the reaction proceeds through direct transmethylation from 38 one MMeHg substituent to another. Solvation effects were found to play an important role in the 39 surface reconstruction of the nanoparticle and in decreasing the energetic barrier for DMeHg 40 formation. We also investigate DMeHg formation from MMeHg mediated by organic dithiols and 41 compare the results to those mediated by the mineral surface. In contrast to the surface reaction, 42 the calculations suggest that dithiol-mediated formation of DMeHg instead proceeds through a 43 mechanism in which Hg–Hg interactions activate a methyl group from one MMeHg substituent 44 for intramolecular transfer to the adjacent MMeHg substituent. These findings refine previously 45 proposed mechanisms of abiotic DMeHg formation and fill gaps in our understanding of global 46 Hg cycling in the environment.
Density Functional Theory Investigation of Oxidation Intermediates on Gold and Gold–Silver Surfaces
Gold and gold-silver alloys can be active and selective oxidation catalysts. Previous work has suggested that O 2 dissociation occurs at bimetallic step sites on gold-silver alloys, but the site responsible for the rest of the reaction steps has not been studied. As a first step in gaining insight into this issue, in this work we investigated the adsorption of oxygen and other oxidation intermediates on the (111) and (211) facets of gold-silver alloys using density functional theory. Oxygen and silver coverage effects were analyzed, and different model structures were compared. We also examined the energy barriers for the diffusion of atomic oxygen to gain insight into O migration and spillover. On (111) surfaces, O adsorption is much stronger at low O coverage (less than 0.22 ML), while on (211) surfaces O is strongly bound at both high and low O coverage. O diffusion across the step is faster than diffusion along the step. Ag stabilizes O, both when directly bound to it and when in an adjacent site. Ag also reduces repulsive O-O interactions at low O coverage. Our calculated reaction barriers for O-assisted CH 3 O dehydrogenation suggest that reaction is faster on steps than on terraces. Overall, our findings suggest that spillover of O from Ag-rich steps to Au-rich terraces does not occur, and that oxidation reactions on gold-silver alloys occurs on step sites. More specifically, oxidation likely occurs either on Ag-rich step sites or on Au-rich step sites that are adjacent to Ag-rich step sites.