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At least 1,567 records · Page 87

Ligand- and Structure-Based Analysis of Deep Learning-Generated Potential α2a Adrenoceptor Agonists

The α2a adrenoceptor is a particularly medically relevant subtype of the G protein-couple receptor family. Unfortunately, high-throughput techniques aimed at producing novel drug leads targeted to this receptor have been largely unsuccessful due to the complex pharmacology of adrenergic receptors. As such, cutting-edge in silico ligand- and structure-based assessment and de novo deep learning methods are well-positioned to provide new insights into protein-ligand interactions and potential active compounds. In this work, we (i) collect a dataset of α2a adrenoceptor agonists and provide it as a resource for the drug design community; (ii) use the dataset as a basis to generate candidate active structures via deep learning; and (iii) apply computational ligand- and structure-based analysis techniques to gain new insight into α2a adrenoceptor agonists and assess the quality of the computer-generated compounds. Additionally, we further describe how such assessment techniques can be applied to putative chemical probes with a case study involved proposed medetomidine-based probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Gyrokinetic simulation of turbulence and transport in the SPARC tokamak

The turbulence and transport expected in the SPARC tokamak Primary Reference Discharge (PRD) [P. Rodriguez-Fernandez et al., J. Plasma Phys. 86, 865860503 (2020)] have been investigated with the gyrokinetic code CGYRO [J. Candy et al., J. Comput. Phys. 324, 73–93 (2016)]. Linear and nonlinear simulations that focus on ion (kθρs<1.0) and electron-scale (kθρs>1.0) turbulence were used to probe the nature of the turbulence and the resulting transport in the fusion core. It is found that in the SPARC PRD, ion temperature gradient (ITG) turbulence is expected to dominate transport over most of the profile with some potential trapped electron mode impact in the near edge. Stiff turbulence is observed over a part of the plasma core such that SPARC's ion temperature profile will likely be pinned to just above the critical gradient for ITG. The role of electromagnetic turbulence, rotation, and electron-scale turbulence was investigated to provide some insight into the physics required to accurately predict SPARC performance via gyrokinetics. Additionally, predictions of impurity peaking for potential low- and high-Z SPARC first-wall materials are probed using ion-scale simulation. The dominance of low-k turbulence in SPARC provides a potential opportunity for more tractable prediction of plasma profiles using nonlinear gyrokinetics. This work is the first step toward full gyrokinetic profile prediction of SPARC kinetic profiles and the resulting fusion power and plasma gain.

Howard, N. T. (ORCID:0000000287876309)↗

Influence of Vane Trailing Edge Flow on the Formation of Cavity Cells and Rim Sealing

Abstract Hot gas ingestion into the turbine rim seal cavity is an important concern for engine designers. To prevent ingestion, rim seals use high-pressure purge flow; however, the penalty is that excessive use of the purge flow decreases engine thermal efficiency. In this paper, a one-stage turbine operating at engine-representative conditions was used to study the effect of steady and time-resolved under-platform cavity temperatures and pressures across a range of coolant flowrates in the presence of vane trailing edge (VTE) flow. This study correlates time-resolved pressure with time-resolved temperature to identify primary frequencies driving ingestion. At certain flowrates, the time-resolved pressures are out of phase with the temperatures, indicating ingestion. Measurements from high-frequency response pressure sensors in the rim seal and vane platform were also used to determine rotational speed and quantity of large-scale structures (cells). In a parallel effort, a computational model using Unsteady Reynolds-averaged Navier–Stokes (URANS) was applied to determine swirl ratio in the rim seal cavity and time-resolved rim sealing effectiveness. The experimental results confirm that at low purge flowrates, the VTE flow influences the unsteady flow field by decreasing pressure unsteadiness in the rim seal cavity. Results show an increase in purge flow increases the number of unsteady large-scale structures in the rim seal and decreases their rotational speed. However, VTE flow was shown to not significantly change the cell speed and count in the rim seal. Simulations point to the importance of the large-scale cell structures in influencing rim sealing unsteadiness, which is not captured in current rim sealing predictive models.

Engineering↗

Computer-aided design file format for additive manufacturing and methods of file generation

A tessellated output file format describing a computer-aided design (CAD) model including a plurality of vertices, a plurality of curves, a plurality of surfaces, and at least one volume, the tessellated output file format comprising base polygon data, a vertex metadata container, a curve metadata container, and a surface metadata container. The base polygon data defines the CAD model for additive manufacturing and includes a plurality of connected polygons, each polygon including a plurality of nodes, a plurality of edges, and a face. The vertex metadata container includes a listing of CAD model vertices and one polygon node associated with each CAD model vertex. The curve metadata container includes a listing of CAD model curves and at least one polygon edge associated with each CAD model curve. The surface metadata container includes a listing of CAD model surfaces and at least one polygon face associated with each CAD model surface.

Vernon, Gregory John↗

Validation of a 4D-PET Maximum Intensity Projection for Delineation of an Internal Target Volume

Purpose: The delineation of internal target volumes (ITVs) in radiation therapy of lung tumors is currently performed by use of either free-breathing (FB) {sup 18}F-fluorodeoxyglucose-positron emission tomography-computed tomography (FDG-PET/CT) or 4-dimensional (4D)-CT maximum intensity projection (MIP). In this report we validate the use of 4D-PET-MIP for the delineation of target volumes in both a phantom and in patients. Methods and Materials: A phantom with 3 hollow spheres was prepared surrounded by air then water. The spheres and water background were filled with a mixture of {sup 18}F and radiographic contrast medium. A 4D-PET/CT scan was performed of the phantom while moving in 4 different breathing patterns using a programmable motion device. Nine patients with an FDG-avid lung tumor who underwent FB and 4D-PET/CT and >5 mm of tumor motion were included for analysis. The 3 spheres and patient lesions were contoured by 2 contouring methods (40% of maximum and PET edge) on the FB-PET, FB-CT, 4D-PET, 4D-PET-MIP, and 4D-CT-MIP. The concordance between the different contoured volumes was calculated using a Dice coefficient (DC). The difference in lung tumor volumes between FB-PET and 4D-PET volumes was also measured. Results: The average DC in the phantom using 40% and PET edge, respectively, was lowest for FB-PET/CT (DCAir = 0.72/0.67, DCBackground 0.63/0.62) and highest for 4D-PET/CT-MIP (DCAir = 0.84/0.83, DCBackground = 0.78/0.73). The average DC in the 9 patients using 40% and PET edge, respectively, was also lowest for FB-PET/CT (DC = 0.45/0.44) and highest for 4D-PET/CT-MIP (DC = 0.72/0.73). In the 9 lesions, the target volumes of the FB-PET using 40% and PET edge, respectively, were on average 40% and 45% smaller than the 4D-PET-MIP. Conclusion: A 4D-PET-MIP produces volumes with the highest concordance with 4D-CT-MIP across multiple breathing patterns and lesion sizes in both a phantom and among patients. Freebreathing PET/CT consistently underestimates ITV when compared with 4D PET/CT for a lesion affected by respiration.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Error estimates to smooth solutions of semi-discrete discontinuous Galerkin methods with quadrature rules for scalar conservation laws

Here, we focus on error estimates to smooth solutions of semi-discrete discontinuous Galerkin (DG) methods with quadrature rules for scalar conservation laws. The main techniques we use are energy estimate and Taylor expansion first introduced by Zhang and Shu in (Zhang and Shu, SIAM J Num Anal 42 (2004), 641–666). We show that, with p K (piecewise polynomials of degree k) finite elements in 1D problems, if the quadrature over elements is exact for polynomials of degree (2k) error estimates of O(h k+1/2 ) are obtained for general monotone fluxes, and optimal estimates of O(h k+1 ) are obtained for upwind fluxes. For multidimensional problems, if in addition quadrature over edges is exact for polynomials of degree (2k+1), error estimates of O(h k ) are obtained for general monotone fluxes, and O(h k+1/2 ) are obtained for monotone and sufficiently smooth numerical fluxes. Numerical results validate our analysis.

97 MATHEMATICS AND COMPUTING↗

Demonstration Trials of AI/ML Edge+Cloud Suite (CRADA Final Report)

PACE AI and LBNL partnered under this CRADA to test and evaluate the PACE5 edge node prototype, an AI/ML edge and cloud-based suite, at FLEXLAB.The objective of the test was to evaluate the PACE5 edge node prototype's ability to perform demand shed and take to dynamic price signals, and to demonstrate advanced fault detection and microgrid monitoring capabilities.

97 MATHEMATICS AND COMPUTING↗

CASMO5 JENDL-4.0 and ENDF/B-VII.1beta4 libraries

This paper details the generation of neutron data libraries for the CASMO5 lattice physics code based on the recently released JENDL-4.0 and ENDF/B-VII.1beta4 nuclear data evaluations. This data represents state-of-the-art nuclear data for late-2011. The key features of the new evaluations are briefly described along with the procedure for processing of this data into CASMO5, 586-energy group neutron data libraries. Finally some CASMO5 results for standard UO{sub 2} and MOX critical experiments for the two new libraries and the current ENDF/B-VII.0 CASMO5 library are presented including the B and W 1810 series, DIMPLE S06A, S06B, TCA reflector criticals with iron plates and the PNL-30-35 MOX criticals. The results show that CASMO5 with the new libraries is performing well for these criticals with a very slight edge in results to the JENDL-4.0 nuclear data evaluation over the ENDF/B-VII.1beta4 evaluation. Work is currently underway to generate a CASMO5 library based on the final ENDF/B-VII.R1 evaluation released Dec. 22, 2011. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Enhancing Clean Energy Innovation Ecosystem Discovery Tool

During March 2016, the DOE’s Office of Energy Policy and Systems Analysis (EPSA) sought a methodology to identify and quantify the strength of the existing clean energy innovation ecosystems (IE) in the U.S. and their characteristics. Oak Ridge National Lab (ORNL) did a pilot study (Phase 1) and demonstrated the feasibility of an application comprised of natural language processing, link analysis, and other computational techniques to transform text and numerical data into metrics on clean energy innovation activity and geography. The data-collection, ingest and analytics pipelines were combined with an advanced user interface, together known as the Ecosystem Discovery Tool, to enhance DOE’s understanding of existing geographic innovation clusters. During Phase 2 of this project, this tool has been further enhanced by integrating new data sets and through backend software architecture changes, validation and bug fixing, making it a much more robust and powerful application. The tool’s user interface is a lot more intuitive, which enables a user to visualize the IE rankings for various geographic regions(CBSA, state level) for different clean energy technologies and seek automated insights. ORNL also created a DOE-specific dashboard that allows the user to visualize and analyze federal funding from various offices including Energy Efficiency and Renewable Energy(EERE), Office of Electricity(OE), Fossil Energy(FE), and Nuclear Energy(NE). During Phase 1 of this project, EPSA defined a clean energy innovation ecosystem as the overlap of five Ecosystem Components: 1) nascent clean energy Indicators, 2) investors, 3) enabling environment, 4) networking assets and 5) large companies. EPSA and ORNL worked together to collect data for each component: 1) small and medium companies, ARPA-E awardees, SBIR awardees, patents, publications, ERCs for Nascent Clean Energy Indicators; 2) qualified investors; 3) the Clean Edge Policy Index/DSIRE for the Enabling Environment; 4) universities, national laboratories, ERCs and incubators for Networking Assets; and 5) large companies and a subset of the Russell 1000 list for Large Companies. The ORNL team created a visual tool based on Tableau that integrated ecosystem component data to score, rank and map IEs. The tool was created with the flexibility to allow the user to choose the weights of each of the five ecosystem components and the subcomponents. This flexibility allows the user to visualize different subsets and to use the underlying data for different types of analysis. During Phase 2 of this project, the backend database and computation process have undergone major changes to provide a much more refined user-interface and added new features into the scoring algorithm. This phase also involved addition of newer databases such as a list of Energy Research Centers (ERC) ,DSIRE, and funding data from EERE, FE, NE, and OE to provide more granular information and more accurate/better quantification.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Interface contributions to topological entanglement in abelian Chern-Simons theory

Here, we study the entanglement entropy between (possibly distinct) topological phases across an interface using an Abelian Chern-Simons description with topological boundary conditions (TBCs) at the interface. From a microscopic point of view, these TBCs correspond to turning on particular gapping interactions between the edge modes across the interface. However, in studying entanglement in the continuum Chern-Simons description, we must confront the problem of non-factorization of the Hilbert space, which is a standard property of gauge theories. We carefully define the entanglement entropy by using an extended Hilbert space construction directly in the continuum theory. We show how a given TBC isolates a corresponding gauge invariant state in the extended Hilbert space, and hence compute the resulting entanglement entropy. We find that the sub-leading correction to the area law remains universal, but depends on the choice of topological boundary conditions. This agrees with the microscopic calculation of [1]. Additionally, we provide a replica path integral calculation for the entropy. In the case when the topological phases across the interface are taken to be identical, our construction gives a novel explanation of the equivalence between the left-right entanglement of (1+1)d Ishibashi states and the spatial entanglement of (2+1)d topological phases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Overdestabilization vs Overstabilization in the Theoretical Analysis of f-Orbital Covalency

The complex nature of the f-orbital electronic structures and their interaction with the chemical environment pose significant computational challenges. Advanced computational techniques that variationally include scalar relativities and spin–orbit coupling directly at the molecular orbital level have been developed to address this complexity. Among these, variational relativistic multiconfigurational multireference methods stand out for their high accuracy and systematic improvement in studies of f-block complexes. Additionally, these advanced methods offer the potential for calibrating low-scaling electronic structure methods such as density functional theory. However, studies on the Cl K-edge X-ray absorption spectra of the [Ce(III)Cl 6 ] 3– and [Ce(IV)Cl 6 ] 2– complexes show that time-dependent density functional theory with approximate exchange–correlation kernels can lead to inaccuracies, resulting in an overstabilization of 4f orbitals and incorrect assessments of covalency. In contrast, approaches utilizing small active space wave function methods may understate the stability of these orbitals. The results herein demonstrate the need for large active space, multireference, and variational relativistic methods in studying f-block complexes.

chemical calculations↗

Codiscovering graphical structure and functional relationships within data: A Gaussian Process framework for connecting the dots

Most problems within and beyond the scientific domain can be framed into one of the following three levels of complexity of function approximation. Type 1: Approximate an unknown function given input/output data. Type 2: Consider a collection of variables and functions, some of which are unknown, indexed by the nodes and hyperedges of a hypergraph (a generalized graph where edges can connect more than two vertices). Given partial observations of the variables of the hypergraph (satisfying the functional dependencies imposed by its structure), approximate all the unobserved variables and unknown functions. Type 3: Expanding on Type 2, if the hypergraph structure itself is unknown, use partial observations of the variables of the hypergraph to discover its structure and approximate its unknown functions. These hypergraphs offer a natural platform for organizing, communicating, and processing computational knowledge. While most scientific problems can be framed as the data-driven discovery of unknown functions in a computational hypergraph whose structure is known (Type 2), many require the data-driven discovery of the structure (connectivity) of the hypergraph itself (Type 3). We introduce an interpretable Gaussian Process (GP) framework for such (Type 3) problems that does not require randomization of the data, access to or control over its sampling, or sparsity of the unknown functions in a known or learned basis. Its polynomial complexity, which contrasts sharply with the super-exponential complexity of causal inference methods, is enabled by the nonlinear ANOVA capabilities of GPs used as a sensing mechanism.

Science & Technology - Other Topics↗

Full coverage shaped-hole film cooling in an accelerating boundary layer with high freestream turbulence

Full coverage shaped-hole film cooling and downstream heat transfer measurements have been acquired in the accelerating flows over a large cylindrical leading edge test surface. The shaped holes had an 8 deg lateral expansion angled at 30 deg to the surface with spanwise and streamwise spacings of 3 diameters. Measurements were conducted at four blowing ratios, two Reynolds numbers, and six well documented turbulence condi-tions. Film cooling measurements were acquired over a four to one range in blowing ratio at the lower Reynolds number and at the two lower blowing ratios for the higher Reynolds number. The film cooling measurements were acquired at a coolant to free-stream density ratio of approximately 1.04. The flows were subjected to a low turbulence (LT) condition (Tu = 0.7%), two levels of turbulence for a smaller sized grid (Tu = 3.5%and 7.9%), one turbulence level for a larger grid (8.1%), and two levels of turbulence generated using a mock aerocombustor (AC) (Tu = 9.3% and 13.7%). Turbulence level is shown to have a significant influence in mixing away film cooling coverage progressively as the flow develops in the streamwise direction. Effectiveness levels for the AC turbu-lence condition are reduced to as low as 20% of LT values by the furthest downstream region. The film cooling discharge is located close to the leading edge with very thin and accelerating upstream boundary layers. Film cooling data at the lower Reynolds number show that transitional flows have significantly improved effectiveness levels compared with turbulent flows. Downstream effectiveness levels are very similar to slot film cooling data taken at the same coolant flow rates over the same cylindrical test surface. However, slots perform significantly better in the near discharge region. These data are expected to be very useful in grounding computational predictions of full coverage shaped-hole film cooling with elevated turbulence levels and acceleration. Lastly, infrared (IR) measurements were performed for the two lowest turbulence levels to document the spanwise variation in film cooling effectiveness and heat transfer.

20 FOSSIL-FUELED POWER PLANTS↗

Full Coverage Shaped Hole Film Cooling in an Accelerating Boundary Layer with High Free-Stream Turbulence

Full coverage shaped-hole film cooling and downstream heat transfer measurements have been acquired in the accelerating flows over a large cylindrical leading edge test surface. The shaped holes had an 8° lateral expansion angled at 30° to the surface with spanwise and streamwise spacings of 3 diameters. Measurements were conducted at four blowing ratios, two Reynolds numbers and six well documented turbulence conditions. Film cooling measurements were acquired over a four to one range in blowing ratio at the lower Reynolds number and at the two lower blowing ratios for the higher Reynolds number. The film cooling measurements were acquired at a coolant to free-stream density ratio of approximately 1.04. The flows were subjected to a low turbulence condition (Tu = 0.7%), two levels of turbulence for a smaller sized grid (Tu = 3.5%, and 7.9%), one turbulence level for a larger grid (8.1%), and two levels of turbulence generated using a mock aero-combustor (Tu = 9.3% and 13.7%). Turbulence level is shown to have a significant influence in mixing away film cooling coverage progressively as the flow develops in the streamwise direction. Effectiveness levels for the aero-combustor turbulence condition are reduced to as low as 20% of low turbulence values by the furthest downstream region. The film cooling discharge is located close to the leading edge with very thin and accelerating upstream boundary layers. Film cooling data at the lower Reynolds number, show that transitional flows have significantly improved effectiveness levels compared with turbulent flows. Downstream effectiveness levels are very similar to slot film cooling data taken at the same coolant flow rates over the same cylindrical test surface. However, slots perform significantly better in the near discharge region. These data are expected to be very useful in grounding computational predictions of full coverage shaped hole film cooling with elevated turbulence levels and acceleration. IR measurements were performed for the two lowest turbulence levels to document the spanwise variation in film cooling effectiveness and heat transfer.

20 FOSSIL-FUELED POWER PLANTS↗

Fingerprinting Uranium Oxides with Electron Energy Loss Spectroscopy Supported by Theoretical Computations

Uranium oxides occur in a variety of phases that differ in crystal structure and uranium oxidation states. Electron energy loss spectroscopy (EELS) is one of the few techniques that has sufficient spatial resolution and sensitivity to electronic structure to distinguish amongst phases at the nanoscale. However, beam-sensitive materials such as uranium oxides are subject to spectral modification due to interactions with the electron beam. Therefore, theory support is essential to reliably exclude the impact of beam damage and generate true reference datasets. Here we use a comparison of theoretical and experimental spectra to probe the impact of beam damage on O K-edge and U N-edge (N6,7 and N4,5) EELS spectra of various single-valent and mixed-valence uranium oxide bulk phases. Using a low-dose experimental set-up, we show that the O K-edge theoretical spectra are in excellent agreement with experiment for both peak positions and relative intensities of respective peaks. In contrast, U N-edge features are less distinguishing due to the partially localized nature of the U 5f orbitals and overlapping multiplet and spin–orbit coupling effects. This work demonstrates that O K-edge EELS is sufficiently diagnostic to distinguish a wide range of uranium oxides and that the experimental approach used here minimizes beam damage and allows valence state discrimination across the U(IV), U(V) and U(VI) series. When combined with imaging modes available in electron mi-croscopy, the work enables detailed investigation and characterization of uranium redox transformations at the nanoscale.

Carbone, Jacopo↗

Not so HOT Triangulations

Here, we propose primal–dual mesh optimization algorithms that overcome shortcomings of the standard algorithm while retaining some of its desirable features. “Hodge-Optimized Triangulations” defines the “HOT energy” as a bound on the discretization error of the diagonalized Delaunay Hodge star operator. HOT energy is a natural choice for an objective function, but unstable for both mathematical and algorithmic reasons: it has minima for collapsed edges, and its extrapolation to non-regular triangulations is inaccurate and has unbounded minima. We propose a different extrapolation with a stronger theoretical foundation, and avoid extrapolation by recalculating the objective just beyond the flip threshold. We propose new objectives, based on normalizations of the HOT energy, with barriers to edge collapses and other undesirable configurations. We propose mesh improvement algorithms coupling these. When HOT optimization nearly collapses an edge, we actually collapse the edge. Otherwise, we use the barrier objective to update positions and weights and remove vertices. By combining discrete connectivity changes with continuous optimization, we more fully explore the space of possible meshes and obtain higher quality solutions.

97 MATHEMATICS AND COMPUTING↗

Calibers: A Bandwidth Calendaring Paradigm for Science Workflows

Many scientific workflows require large data transfers between distributed instrument facilities, storage and computing resources. To ensure that these resources are maximally utilized, R&E networks connecting these resources must ensure that an inherently unpredictable network behaves predictably. In practice, this amounts to the per-application over-provisioning of network resources in an attempt to guarantee that adequate throughput is provided to users. This often results in resource under-utilization over time. One promising solution is the use of deadlines and bandwidth calendaring. In this approach, "fair" resource allocation is replaced with deadline-based resource allocation. However, these approaches often suffer from issues in efficiently regulating resource allocation and failure modes. Therefore, our solution, Calibers, approaches bandwidth calendaring and deadline-awareness in a different way. Calibers uses shaping, metering, and pacing at the edge of the network and end-system to provide participating clients the ability to schedule bandwidth reservations without having to worry about network noise from non-participating clients. Calibers can also fail back to the fair resource allocation of underlying transport protocols if necessary. For example, if a non-participating flow somehow enters the core of the network, or a sudden network change causes the available bandwidth to be exceeded, the underlying transport protocol congestion avoidance implementation will be able to handle the congestion as it normally would. Furthermore, Calibers provides a novel simulation method and resource allocation algorithm.

97 MATHEMATICS AND COMPUTING↗

Exploring the Coexistence of Spin States in [Fe(tpy-Ph) 2 ] 2+ Complexes on Au(111) Using DFT Calculations

In this work, we systematically study the electronic structure and stability of spin states of the [Fe-(tpy-ph) 2 ] 2+ molecule in both the gas phase and on a Au(111) substrate using density functional theory + U (DFT+ U ) calculations. We find that the stability of the Fe 2+ ion’s spin states predicted by the computations is significantly influenced by the Hubbard U parameter. In the gas phase, the low-spin (LS, S = 0) state is found to be energetically favorable for U (Fe) ≤ 3 eV, whereas the high-spin (HS, S = 2) state is stabilized for U (Fe) > 3 eV. Interaction with the Au(111) substrate is found to elevate the critical U for the spin-state transition to 3.5 eV. Additionally, we perform L-edge X-ray absorption spectroscopy (XAS) calculations for both HS and LS states. The calculated XAS suggests that the HS state more closely aligns with the experimental observations, indicating the potential coexistence of the HS state as the initial state during the X-ray excitation process. These findings enrich our understanding of spin-state dynamics in [Fe(tpy-Ph) 2 ] 2+ .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗