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Nearest neighbor approaches and a new neural network, the Binary Diamond, are used for the classification of images of ground pixels obtained by LANDSAT satellite. The performances are evaluated by comparing classifications of a scene in the vicinity of Washington DC. The problem of optimal selection of categories is addressed as a step in the classification process.
This project focused on the development bimetallic metal-organic frameworks (MOFs) as gas phase heterogeneous catalysts for hydrogenation and hydroformylation reactions. MOFs are a new class of hybrid inorganic/organic materials that are highly crystalline, with structures consisting of metal nodes of specific geometries connected by organic linkers. Although there have been a number of studies of catalysis at MOF nodes in solution, there is little experimental data in the literature for gas phase reactions despite the fact that industrial heterogeneous catalysis on MOFs is more economically viable than homogeneous catalysis. The use of MOFs as heterogeneous catalysts presents the unique opportunity to carefully control the composition, geometry and ensemble sizes of the active sites, which are all critical factors for the rational design of new catalysts. Specific objectives of the project are as follows: (1) to tailor the geometry, composition and ensemble size of the active sites; (2) to understand how the adsorption of molecules at metal sites can be modified by interactions with a neighboring metal site; (3) to determine how oxidation states of the metal change during reaction and how these states can be modified by metal-metal electronic interactions; and (4) to elucidate reaction mechanisms and intermediates. For these studies, we have chosen to investigate selective hydrogenation of hydrocarbons and hydroformylation, which are industrially relevant reactions. Our interdisciplinary team of Chen, Shustova and Vogiatzis/Henkelman provides critical expertise in novel MOF synthesis (Shustova), atomic-scale surface science and catalysis (Chen) and computational studies of reaction mechanisms (Vogiatzis/Henkelman) that are necessary for the development of these catalysts. We believe that this work will lead directly to the rational design of new catalysts that are versatile, highly active/selective and suitable for industrial processes.
A nonlinear Lagrangian formulation for the spatial kinematic and dynamic analysis of open chain deformable links consisting of cylindrical joints that connect pairs of flexible links is developed. The special cases of revolute or prismatic joint can also be obtained from the kinematic equations. The kinematic equations are described using a 4x4 matrix method. The configuration of each deformable link in the open loop kinematic chain is identified using a coupled set of relative joint variables, constant geometric parameters, and elastic coordinates. The elastic coordinates define the link deformation with respect to a selected joint coordinate system that is consistent with the kinematic constraints on the boundary of the deformable link. These coordinates can be introduced using approximation techniques such as Rayleigh-Ritz method, finite element technique or any other desired approach. The large relative motion between two neighboring links are defined by a set of joint coordinates which describes the large relative translational and rotational motion between two neighboring joint coordinate systems. The origin of these coordinate systems are rigidly attached to the neighboring links at the joint definition points along the axis of motion.
Visualization of time-varying volumetric data sets, which may be obtained from numerical simulations or sensing instruments, provides scientists insights into the detailed dynamics of the phenomenon under study. This paper describes a coherent solution based on quantization, coupled with octree and difference encoding for visualizing time-varying volumetric data. Quantization is used to attain voxel-level compression and may have a significant influence on the performance of the subsequent encoding and visualization steps. Octree encoding is used for spatial domain compression, and difference encoding for temporal domain compression. In essence, neighboring voxels may be fused into macro voxels if they have similar values, and subtrees at consecutive time steps may be merged if they are identical. The software rendering process is tailored according to the tree structures and the volume visualization process. With the tree representation, selective rendering may be performed very efficiently. Additionally, the I/O costs are reduced. With these combined savings, a higher level of user interactivity is achieved. We have studied a variety of time-varying volume datasets, performed encoding based on data statistics, and optimized the rendering calculations wherever possible. Preliminary tests on workstations have shown in many cases tremendous reduction by as high as 90% in both storage space and inter-frame delay.
In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.
Extended X ray absorption fine structure (EXAFS) is a powerful technique for probing the local atomic structure of battery and fuel cell materials. The major advantages of EXAFS are that both the probe and the signal are X rays and the technique is element selective and applicable to all states of matter. This permits in situ studies of electrodes and determination of the structure of single components in composite electrodes, or even complete cells. EXAFS specifically probes short range order and yields coordination numbers, bond distances, and chemical identity of nearest neighbors. Thus, it is ideal for structural studies of ions in solution and the poorly crystallized materials that are often the active materials or catalysts in batteries and fuel cells. Studies on typical battery and fuel cell components are used to describe the technique and the capability of EXAFS as a structural tool in these applications. Typical experimental and data analysis procedures are outlined. The advantages and limitations of the technique are also briefly discussed.
Hydrodynamic diffusion refers to the fluctuating motion of nonBrownian particles (or droplets or bubbles) which occurs in a dispersion due to multiparticle interactions. For example, in a concentrated sheared suspension, particles do not move along streamlines but instead exhibit fluctuating motions as they tumble around each other. This leads to a net migration of particles down gradients in particle concentration and in shear rate, due to the higher frequency of encounters of a test particle with other particles on the side of the test particle which has higher concentration or shear rate. As another example, suspended particles subject to sedimentation, centrifugation, or fluidization, do not generally move relative to the fluid with a constant velocity, but instead experience diffusion-like fluctuations in velocity due to interactions with neighboring particles and the resulting variation in the microstructure or configuration of the suspended particles. In flowing granular materials, the particles interact through direct collisions or contacts (rather than through the surrounding fluid); these collisions also cause the particles to undergo fluctuating motions characteristic of diffusion processes. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.
Extensive measurements are made in a transitioning swept-wing boundary layer using hot-film, hot-wire and cross-wire anemometry. The crossflow-dominated flow contains stationary vortices that breakdown near mid-chord. The most amplified vortex wavelength is forced by the use of artificial roughness elements near the leading edge. Two-component velocity and spanwise surface shear-stress correlation measurements are made at two constant chord locations, before and after transition. Streamwise surface shear stresses are also measured through the entire transition region. Correlation techniques are used to identify stationary structures in the laminar regime and coherent structures in the turbulent regime. Basic techniques include observation of the spatial correlations and the spatially distributed auto-spectra. The primary and secondary instability mechanisms are identified in the spectra in all measured fields. The primary mechanism is seen to grow, cause transition and produce large-scale turbulence. The secondary mechanism grows through the entire transition region and produces the small-scale turbulence. Advanced techniques use Linear Stochastic Estimation (LSE) and Proper Orthogonal Decomposition (POD) to identify the spatio-temporal evolutions of structures in the boundary layer. LSE is used to estimate the instantaneous velocity fields using temporal data from just two spatial locations and the spatial correlations. Reference locations are selected using maximum RMS values to provide the best available estimates. POD is used to objectively determine modes characteristic of the measured flow based on energy. The stationary vortices are identified in the first laminar modes of each velocity component and shear component. Experimental evidence suggests that neighboring vortices interact and produce large coherent structures with spanwise periodicity at double the stationary vortex wavelength. An objective transition region detection method is developed using streamwise spatial POD solutions which isolate the growth of the primary and secondary instability mechanisms in the first and second modes, respectively. Temporal evolutions of dominant POD modes in all measured fields are calculated. These scalar POD coefficients contain the integrated characteristics of the entire field, greatly reducing the amount of data to characterize the instantaneous field. These modes may then be used to train future flow control algorithms based on neural networks.
Single-atom catalysts (SACs) are gaining increasing recognition because of their superior catalytic properties for various reactions. However, the performance of SACs is often limited by the lack of neighboring metal centers to cooperate in catalysis. Herein, a synergetic interaction between neighboring Cu atoms of a few-atom catalyst (FAC) on graphdiyne is found to greatly enhance the production of acetate in CO electroreduction reaction relative to Cu SACs. In a 1.0 M KOH electrolyte, this Cu FAC exhibits an acetate Faradaic efficiency of 53.8±1.5 % and an ultrahigh relative purity of up to 97 wt% for liquid products, and excellent stability of over 23 h continuous electrolysis at -0.8 V versus reversible hydrogen electrode (RHE). Theoretical studies suggest that the intersite catalytic communication between two neighboring metal atoms confined in each pore of GDY facilitates the formation of acetic acid through either stepwise hydrogenation of CH 2 CO* or the direct reaction of H 2 O with CH 2 CO*. Our study demonstrates the unprecedented synergetic catalysis of Cu FAC in promoting the selective CO electroreduction toward acetate production.
Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana . A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.
In the variational subspace valence bond (VSVB) [G. D. Fletcher, J. Chem. Phys. 142, 134112 (2015)] method, the electronic orbitals comprising the wave function correspond to chemically meaningful objects, such as bonds, lone pairs, atomic cores, and so on. Selected regions of a molecule (for example, a single chemical bond, as opposed to all the bonds) can be modeled with different levels of basis set and possible methods for modeling correlation from the other regions. The interactions between the components of a molecule (say, a bond and a neighboring orbital) can then be studied in detail for their impact on a chemical phenomenon while avoiding the expense of necessarily applying the higher levels and methods to the entire molecule. Here, this work presents the theoretical basis for modeling correlation effects between specific electron pairs by incorporating terms in the inter-electronic coordinates (“r 12 ”) into VSVB. The approach is validated with calculations on small systems using single-reference wave functions.
Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.
The paper concentrates on a linear approximation method for predicting the changes occurring in steady-state numerical solutions of the Euler equations as a consequence of small changes in the independent variables which control the problem. The importance of proper boundary-condition treatment and other issues concerning the problem are covered along with the importance of proper algorithm selection for a fully supersonic inviscid flow. The method is applied to a subsonic nozzle involving variation of the pressure on the outflow boundary and to a supersonic inlet involving variation of the inflow Mach number. In the subsonic test case, the comparisons between the predicted and conventional numerical solutions are shown to be good, while in the supersonic test case, the agreement between the approximation method and conventional numerical solution starts out well but rapidly degenerates at some point in the flowfield as the perturbation of the boundary conditions is increased.
5-Thioglycopyranosyl donors differ in reactivity and selectivity from simple glycopyranosyl donors. An extensive study has been conducted on the nature and stability of the reactive intermediates generated on the activation of per-O-acetyl and per-O-methyl 5-thioglucopyranosyl donors and the corresponding glucopyranosyl donors. Variable temperature nuclear magnetic resonance (NMR) studies with per-O-methylated or per-O-acetyl glycosyl sulfoxides and trichloroacetimidates on activation with trifluoromethanesulfonic anhydride or trimethylsilyl triflate are reported. These show that following initial adduct formation with the promoter conversion of the 5-thioglucopyranosyl donors to the 5-thioglucopyranosyl triflates requires higher temperatures than that of the glucopyranosyl donors to the glucopyranosyl triflates. It is demonstrated that neighboring group participation is a less important phenomenon for the peracetylated thioglucosyl donors than for the peracetylated glucosyl donors. A simple thiocarbenium ion was generated by protonation of 2,3-dihydro-4H-thiopyran at low temperature and characterized by NMR spectroscopy. However, the corresponding 5-thioglucopyranosyl thenium ions were not observed in any of the NMR studies of the 5-thiopyranosyl donors: the electron-withdrawing C–O bonds around the thiopyranoside core discourage thiocarbenium ion formation, just as they discourage oxocarbenium ion formation. Density functional theory (DFT) calculations reveal the tetrahydrothiopyranyl thiocarbenium ion to be approximately 2.5 kcal/mol lower in energy than the corresponding tetrahydropyranyl oxocarbenium ion relative to the corresponding covalent triflates. However, the computations reveal a 5.8 kcal/mol activation barrier for conversion of the tetrahydrothiopyranyl triflate to the thiocarbenium ion, while formation of the oxocarbenium ion–triflate ion pair from tetrahydropyranyl triflate requires only 2.6 kcal·mol –1 . Overall, the greater axial selectivity of 5-thioglycopyranosyl donors compared to analogous glycopyranosyl donors derives from (i) the lower kinetic reactivity necessitating higher reaction temperatures, (ii) the greater stability of the thiocarbenium ion over the oxocarbenium ion facilitating equilibration under thermodynamic conditions, (iii) the greater magnitude of the anomeric effect in the 5-thiosugars, and (iv) decreased neighboring group participation in the per-esterified 5-thiosugars.
The CATOFIN© process produces propylene from propane using a CrO x /Al 2 O 3 catalyst. Despite its use, there are still uncertainties surrounding the nature of Cr species formed during synthesis, regeneration, and aging. It has been observed that ppm levels of Cr 2 O 3 can be oxidized to Cr(VI) in air; however, when Cr 2 O 3 is in direct contact with Al 2 O 3 , Cr(VI) formation increased more than 100-fold. Here, to confirm physical contact between Cr 2 O 3 and Al 2 O 3 results in increased Cr(VI) formation, Cr 2 O 3 and Cr 2 O 3 /Al 2 O 3 samples were synthesized, calcined, and characterized. Catalytic activity measurements confirm propylene selectivity inversely tracks with Cr(VI). Wet chemical titration and X-ray absorption spectroscopy (XAS) quantified and determined the structure of the Cr(VI) species. FEFF X-ray absorption near edge structure simulations determined the potential sensitivity of the XAS to the presence of Al 3+ /Cr 3+ neighboring atoms. XAS correlated to FEFF simulations suggested that Al 3+ x Cr 3+ 2–x Cr 6+ 3 O 12 comprises a significant fraction of the Cr(VI) species formed.
Inherently disordered structures of carbon nitrides have hindered an atomic level tunability and understanding of their catalytic reactivity. Starting from a crystalline carbon nitride, poly(triazine imide) or PTI/LiCl, the coordination of copper cations to its intralayer N-triazine groups was investigated using molten salt reactions. The reaction of PTI/LiCl within CuCl or eutectic KCl/CuCl 2 molten salt mixtures at 280 to 450 °C could be used to yield three partially disordered and ordered structures, wherein the Cu cations are found to coordinate within the intralayer cavities. Local structural differences and the copper content, i.e., whether full or partial occupancy of the intralayer cavity occurs, were found to be dependent on the reaction temperature and Cu-containing salt. Crystallites of Cu-coordinated PTI were also found to electrophoretically deposit from aqueous particle suspensions onto either graphite or FTO electrodes. As a result, electrocatalytic current densities for the reduction of CO 2 and H 2 O reached as high as ∼10 to 50 mA cm −2 , and remained stable for >2 days. Selectivity for the reduction of CO 2 to CO vs. H 2 increases for thinner crystals as well as for when two Cu cations coordinate within the intralayer cavities of PTI. Mechanistic calculations have also revealed the electrocatalytic activity for CO 2 reduction requires a smaller thermodynamic driving force with two neighboring Cu atoms per cavity as compared to a single Cu atom. These results thus establish a useful synthetic pathway to metal-coordination in a crystalline carbon nitride and show great potential for mediating stable CO 2 reduction at sizable current densities.
A solution adaptive grid procedure based on an error equi-distribution scheme is developed and applied to a Parabolized Navier-Stokes solver. An improved method for selecting weighting functions is introduced which involves normalizing a combination of flowfield gradients and curvature of a number of dependent variables and then selecting the largest at each point. The scheme re-distributes grid points line-by-line, with grid point motion controlled by forces analogous to tensional and torsional spring forces with the spring constants set equal to the weighting functions. Torsional terms are functions of the grid point positions along neighboring grid lines and provide grid smoothness and stability. A grid-fitting scheme is introduced for external flows in which the number of grid points in the freestream are reduced to a minimum. Results for several problems are presented to demonstrate the improvements obtainable with the solution adaptive grid procedure.
The FORTRAN programs supplied in this document provide a complete processing package for statistically extracting residual core, external field and lithospheric components in Magsat observations. To process the individual passes: (1) orbits are separated into dawn and dusk local times and by altitude, (2) passes are selected based on the variance of the magnetic field observations after a least-squares fit of the core field is removed from each pass over the study area, and (3) spatially adjacent passes are processed with a Fourier correlation coefficient filter to separate coherent and non-coherent features between neighboring tracks. In the second state of map processing: (1) data from the passes are normalized to a common altitude and gridded into dawn and dusk maps with least squares collocation, (2) dawn and dusk maps are correlated with a Fourier correlation efficient filter to separate coherent and non-coherent features; the coherent features are averaged to produce a total field grid, (3) total field grids from all altitudes are continued to a common altitude, correlation filtered for coherent anomaly features, and subsequently averaged to produce the final total field grid for the study region, and (4) the total field map is differentially reduced to the pole.