Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad
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Kumar, Prashasti↗
SEARCH · Engineering Papers
Results for “Geometric adaptivity”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Adaptive multisensor fusion for planetary exploration rovers
The purpose of the adaptive multisensor fusion system currently being designed at NASA/Johnson Space Center is to provide a robotic rover with assured vision and safe navigation capabilities during robotic missions on planetary surfaces. Our approach consists of using multispectral sensing devices ranging from visible to microwave wavelengths to fulfill the needs of perception for space robotics. Based on the illumination conditions and the sensors capabilities knowledge, the designed perception system should automatically select the best subset of sensors and their sensing modalities that will allow the perception and interpretation of the environment. Then, based on reflectance and emittance theoretical models, the sensor data are fused to extract the physical and geometrical surface properties of the environment surface slope, dielectric constant, temperature and roughness. The theoretical concepts, the design and first results of the multisensor perception system are presented.
Collin, Marie-France↗
Study and design of the ion cyclotron resonance heating system for the stellarator Wendelstein 7-X
The current status of the mechanical and electromagnetic design for the ICRF antenna system for W7-X is presented. Two antenna plugins are discussed: one consisting of a pair of straps with pre-matching to cover the first frequency band, 25–38 MHz, and a second one consisting of two short strap triplets to cover a frequency band around 76 MHz. This paper focusses on the two strap antenna for the lower frequency band. Power coupling of the antenna to a reference plasma profile is studied with the help of the codes TOPICA and Microwave Studio that deliver the scattering matrix needed for the optimization of the geometric parameters of the straps and antenna box. Radiation power spectra for different phasings of the two straps are obtained using the code ANTITER II and different heating scenario are discussed. The potential for heating, fast particle generation, and current drive is discussed. The problem of RF coupling through the plasma edge and of edge power deposition is summarized. Important elements of the complete ion cyclotron resonance heating system are discussed: a resonator circuit with tap feed to limit the maximum voltage in the system, and a decoupler to counterbalance the large mutual coupling between the 2 straps. The mechanical design highlights the challenges encountered with this antenna: adaptation to a large variety of plasma configurations, the limited space within the port to accommodate the necessary matching components and the watercooling needed for long pulse operation.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Quantification of LEU Holdup using gamma ray imaging and inverse transport solver
Holdup is the residual amount of special nuclear material (SNM) remaining in a processing facility after the bulk materials have been cleaned out. In commercial uranium processing facilities, quantification of holdup is a major challenge because of the highly variable shapes and sizes of the deposits. Any method that attempts to generalize and calibrate deposit shapes in order to quantify holdup will be prone to high uncertainties. Uncertainties on the order of ±50% are typical in holdup results. In international safeguards applications, a ±50% uncertainty can result in a large amount of material unaccounted for (MUF) thereby increasing the difficulty of detecting material diversion and facility misuse. An imaging-based methodology has been developed with the objective of significantly reducing this uncertainty by using the true deposit shape, instead of relying on oversimplified geometric assumptions. The project is a collaboration between ORNL, Y-12, and the University of Tennessee, Knoxville, TN. Uranium sources of known masses were measured using the Germanium Gamma-ray Imager (GeGI), a high-resolution imaging spectrometer, creating a pixelated map for each spectral bin. Two different gamma imaging methods are employed in this work: coded aperture imaging and Compton imaging. A validated MonteCarlo model of the detector has been developed using the GEANT4 code for determining the intrinsic response of the detector, its enclosure, and the coded aperture mask. An inverse transport solver based on the Markov Chain Monte-Carlo approach known as Differential Evolution Adaptive Metropolis (DREAM) is employed to use the measurement data from the image pixels (coded aperture or Compton) to solve for the mass of 235 U in the deposit. A reliable method based on the DREAM solver has been developed to flag the infinite thickness condition of a uranium deposit. The project team is working towards improving the image reconstruction for Compton imaging so that a better localization of the source can be achieved. Besides treating the coded aperture and Compton imaging methods independently, the project is also evaluating a combined method that uses the Compton scatter data from a coded aperture measurement. GEANT4 simulations are being performed to evaluate the combined approach. The impact on the DREAM optimization as the source thickness progressively approaches infinite thickness is being evaluated. A number of uranium sources available at ORNL have been measured, and the DREAM results have been tested and validated for the coded aperture imaging. A similar effort will be carried out to validate the Compton based method once the development of algorithms for better localization are complete. The imaging based quantification is very amenable to unattended monitoring of holdup accumulation at key measurement points. A proof of concept measurement has been completed to demonstrate this capability The current work used the high energy resolution imager GeGI. However, the approach and methodologies are applicable to other imagers such as the cadmium zin telluride (CZT) based imager manufactured by H3D, Inc.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Predictive Treatment Management: Incorporating a Predictive Tumor Response Model Into Robust Prospective Treatment Planning for Non-Small Cell Lung Cancer
Purpose: We hypothesized that a treatment planning technique that incorporates predicted lung tumor regression into optimization, predictive treatment planning (PTP), could allow dose escalation to the residual tumor while maintaining coverage of the initial target without increasing dose to surrounding organs at risk (OARs). Methods and Materials: We created a model to estimate the geometric presence of residual tumors after radiation therapy using planning computed tomography (CT) and weekly cone beam CT scans of 5 lung cancer patients. For planning purposes, we modeled the dynamic process of tumor shrinkage by morphing the original planning target volume (PTV{sub orig}) in 3 equispaced steps to the predicted residue (PTV{sub pred}). Patients were treated with a uniform prescription dose to PTV{sub orig}. By contrast, PTP optimization started with the same prescription dose to PTV{sub orig} but linearly increased the dose at each step, until reaching the highest dose achievable to PTV{sub pred} consistent with OAR limits. This method is compared with midcourse adaptive replanning. Results: Initial parenchymal gross tumor volume (GTV) ranged from 3.6 to 186.5 cm{sup 3}. On average, the primary GTV and PTV decreased by 39% and 27%, respectively, at the end of treatment. The PTP approach gave PTV{sub orig} at least the prescription dose, and it increased the mean dose of the true residual tumor by an average of 6.0 Gy above the adaptive approach. Conclusions: PTP, incorporating a tumor regression model from the start, represents a new approach to increase tumor dose without increasing toxicities, and reduce clinical workload compared with the adaptive approach, although model verification using per-patient midcourse imaging would be prudent.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Integration of the Radiation Belt Environment Model Into the Space Weather Modeling Framework
We have integrated the Fok radiation belt environment (RBE) model into the space weather modeling framework (SWMF). RBE is coupled to the global magnetohydrodynamics component (represented by the Block-Adaptive-Tree Solar-wind Roe-type Upwind Scheme, BATS-R-US, code) and the Ionosphere Electrodynamics component of the SWMF, following initial results using the Weimer empirical model for the ionospheric potential. The radiation belt (RB) model solves the convection-diffusion equation of the plasma in the energy range of 10 keV to a few MeV. In stand-alone mode RBE uses Tsyganenko's empirical models for the magnetic field, and Weimer's empirical model for the ionospheric potential. In the SWMF the BATS-R-US model provides the time dependent magnetic field by efficiently tracing the closed magnetic field-lines and passing the geometrical and field strength information to RBE at a regular cadence. The ionosphere electrodynamics component uses a two-dimensional vertical potential solver to provide new potential maps to the RBE model at regular intervals. We discuss the coupling algorithm and show some preliminary results with the coupled code. We run our newly coupled model for periods of steady solar wind conditions and compare our results to the RB model using an empirical magnetic field and potential model. We also simulate the RB for an active time period and find that there are substantial differences in the RB model results when changing either the magnetic field or the electric field, including the creation of an outer belt enhancement via rapid inward transport on the time scale of tens of minutes.
Glocer, A.↗
Assessing impacts of canopy 3D structure on chlorophyll fluorescence radiance and radiative budget of deciduous forest stands using DART
Although remote sensing (RS) of solar-induced chlorophyll fluorescence (SIF) is increasingly used as a valuable source of information about vegetation photosynthetic activity, the RS SIF observations are significantly influenced by canopy-specific structural features (i.e., canopy architecture including leaf area index and presence of woody components), atmospheric conditions during their acquisition (e.g., proportion of direct and diffuse irradiance) and observational geometric configurations (e.g., sun and viewing directions). Radiative transfer (RT) models have the potential to provide a better understanding of the canopy structural effects on the SIF emission and RS signals. Here, we used the DART model to assess the daily influence, from morning to evening, of forest 3D architecture on SIF nadir radiance, emission, escape factor and nadir yield of eight 100 m × 100 m forest study plots established in a temperate deciduous forest of the Smithsonian Environmental Research Center (Edgewater, MD, USA). The 3D architecture of each plot was derived from airborne LiDAR. DART simulations of these 3D forest plots and their 1D (i.e., vertical profile of sun-adapted and shade-adapted leaves) and 0D (i.e., homogeneous layer of sun-adapted leaves above an homogeneous layer of shade-adapted leaves) abstractions were compared to assess the relative errors (ε1D−3D and ε0D−3D) associated with horizontal and vertical structural heterogeneity, respectively. Forest 3D structure, especially horizontal heterogeneity, had a great influence on forest nadir SIF radiance, resulting in ε1D−3D up to 55% at 8:00 and 18:00 (i.e., for oblique sun directions). The key indicators of this impact, in the descending order of importance, were the SIF escape factor (ε1D−3D up to 40%), the attenuation of incident photosynthetically active radiation (ε1D−3D less than 5%), and the SIF emission yield (ε1D−3D less than 2%). The influence of forest architecture on the nadir SIF escape factor and SIF yield (ε1D−3D up to 40%) varied over time, with differences in forest stand structure, and per spectral domain, being always larger between 640 and 700 nm than between 700 and 850 nm. In addition, woody elements demonstrated a large influence on forest SIF radiance due to their “shading” effect (ε up to 17%) and their “blocking” effect (ε ≈ 10%), both of them higher for far-red than for red SIF. These results underline the importance of 3D forest canopy architecture, especially 2D heterogeneity, and inclusion of woody elements in RT modeling used for interpretation of the RS SIF signal, and subsequently for the estimation of gross primary production and detection of vegetation stress.
Omar Regaieg↗
CAGI: Computer Aided Grid Interface. A work in progress
Progress realized in the development of a Computer Aided Grid Interface (CAGI) software system in integrating CAD/CAM geometric system output and/or Interactive Graphics Exchange Standard (IGES) files, geometry manipulations associated with grid generation, and robust grid generation methodologies is presented. CAGI is being developed in a modular fashion and will offer fast, efficient and economical response to geometry/grid preparation, allowing the ability to upgrade basic geometry in a step-by-step fashion interactively and under permanent visual control along with minimizing the differences between the actual hardware surface descriptions and corresponding numerical analog. The computer code GENIE is used as a basis. The Non-Uniform Rational B-Splines (NURBS) representation of sculptured surfaces is utilized for surface grid redistribution. The computer aided analysis system, PATRAN, is adapted as a CAD/CAM system. The progress realized in NURBS surface grid generation, the development of IGES transformer, and geometry adaption using PATRAN will be presented along with their applicability to grid generation associated with rocket propulsion applications.
Soni, Bharat K.↗
Straight Line Geometric Path Lengths – Examples and Distributions
The straight line geometric path distribution of different shapes is a fundamental parameter of any a detector sensitive and in the presence of high energy charged particles such as galactic cosmic rays (GCRs). Knowledge of the straight line path distribution can yield first estimates of the expected energy distribution due to minimum ionizing particles. This predicted shape provides a valuable interpretation tool of spectra of particles that are unlikely to stop in a detector and may present a background or desired signal. These quantities have been calculated many times before including analytically, Coleman (1973), and even in Geant4 software, (Agostinelli, Allison et al. 2003, Santin, Ivanchenko et al. 2005). For this work we utilize the Rapid Adaptable Multi-threaded Particle and Radiation Transport (RAMPART) simulation framework and collect some common shapes all with the same volume to serve as a reference of path lengths and instructions manual for computing other shapes as desired.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Parallel automated adaptive procedures for unstructured meshes
Consideration is given to the techniques required to support adaptive analysis of automatically generated unstructured meshes on distributed memory MIMD parallel computers. The key areas of new development are focused on the support of effective parallel computations when the structure of the numerical discretization, the mesh, is evolving, and in fact constructed, during the computation. All the procedures presented operate in parallel on already distributed mesh information. Starting from a mesh definition in terms of a topological hierarchy, techniques to support the distribution, redistribution and communication among the mesh entities over the processors is given, and algorithms to dynamically balance processor workload based on the migration of mesh entities are given. A procedure to automatically generate meshes in parallel, starting from CAD geometric models, is given. Parallel procedures to enrich the mesh through local mesh modifications are also given. Finally, the combination of these techniques to produce a parallel automated finite element analysis procedure for rotorcraft aerodynamics calculations is discussed and demonstrated.
Shephard, M. S.↗
Multi-Level Structural Damage Characterization Using Sparse Acoustic Sensor Networks and Knowledge Transferred Deep Learning
Standard structural health monitoring techniques face well-known difficulties for comprehensive defect diagnosis in real-world structures that have structural, material, or geometric complexity. This motivates the exploration of machine-learning-based structural health monitoring methods in complex structures. However, creating sufficient training data sets with various defects is an ongoing challenge for data-driven machine (deep) learning algorithms. The ability to transfer the knowledge of a trained neural network from one component to another or to other sections of the same component would drastically reduce the required training data set. Also, it would facilitate computationally inexpensive machine learning based inspection systems. In this work, a machine-learning-based multi-level damage characterization is demonstrated with the ability to transfer trained knowledge within the sparse sensor network. A novel network spatial assistance and an adaptive convolution technique are proposed for efficient knowledge transfer within the deep learning algorithm. Proposed structural health monitoring method is experimentally evaluated on an aluminum plate with artificially induced defects. It was observed that the method improves the performance of knowledge transferred damage characterization by 50% during localization and 24% during severity assessment. Further, experiments using time windows with and without multiple edge reflections are studied. Results reveal that multiply scattered waves contain rich and deterministic defect signatures that can be mined using deep learning neural networks, improving the accuracy of both identification and quantification. In the case of a fixed sensor network, using multiply scattered waves shows 100% prediction accuracy at all levels of damage characterization.
36 MATERIALS SCIENCE↗
A micromirror array with annular partitioning for high-speed random-access axial focusing
Dynamic axial focusing functionality has recently experienced widespread incorporation in microscopy, augmented/virtual reality (AR/VR), adaptive optics and material processing. However, the limitations of existing varifocal tools continue to beset the performance capabilities and operating overhead of the optical systems that mobilize such functionality. The varifocal tools that are the least burdensome to operate (e.g. liquid crystal, elastomeric or optofluidic lenses) suffer from low (≈100 Hz) refresh rates. Conversely, the fastest devices sacrifice either critical capabilities such as their dwelling capacity (e.g. acoustic gradient lenses or monolithic micromechanical mirrors) or low operating overhead (e.g. deformable mirrors). Here, we present a general-purpose random-access axial focusing device that bridges these previously conflicting features of high speed, dwelling capacity and lightweight drive by employing low-rigidity micromirrors that exploit the robustness of defocusing phase profiles. Geometrically, the device consists of an 8.2 mm diameter array of piston-motion and 48-μm-pitch micromirror pixels that provide 2π phase shifting for wavelengths shorter than 1100 nm with 10–90% settling in 64.8 μs (i.e., 15.44 kHz refresh rate). The pixels are electrically partitioned into 32 rings for a driving scheme that enables phase-wrapped operation with circular symmetry and requires <30 V per channel. Optical experiments demonstrated the array’s wide focusing range with a measured ability to target 29 distinct resolvable depth planes. Overall, the features of the proposed array offer the potential for compact, straightforward methods of tackling bottlenecked applications, including high-throughput single-cell targeting in neurobiology and the delivery of dense 3D visual information in AR/VR.
42 ENGINEERING↗
Measuring stomatal and guard cell metrics for plant physiology and growth using StoManager1
Abstract Automated guard cell detection and measurement are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Most current methods for measuring guard cells and stomata are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing geometrical, mathematical algorithms, and convolutional neural networks to automatically detect, count, and measure over 30 guard cell and stomatal metrics, including guard cell and stomatal area, length, width, stomatal aperture area/guard cell area, orientation, stomatal evenness, divergence, and aggregation index. Combined with leaf functional traits, some of these StoManager1-measured guard cell and stomatal metrics explained 90% and 82% of tree biomass and intrinsic water use efficiency (iWUE) variances in hardwoods, making them substantial factors in leaf physiology and tree growth. StoManager1 demonstrated exceptional precision and recall (mAP@0.5 over 0.96), effectively capturing diverse stomatal properties across over 100 species. StoManager1 facilitates the automation of measuring leaf stomatal and guard cells, enabling broader exploration of stomatal control in plant growth and adaptation to environmental stress and climate change. This has implications for global gross primary productivity (GPP) modeling and estimation, as integrating stomatal metrics can enhance predictions of plant growth and resource usage worldwide. Easily accessible open-source code and standalone Windows executable applications are available on a GitHub repository (https://github.com/JiaxinWang123/StoManager1) and Zenodo (https://doi.org/10.5281/zenodo.7686022).
Wang, Jiaxin (ORCID:0000000348085085)↗
Final Report - Subcontract B6183769
During my visit to LLNL during July 5{15, 2016, we worked on linear system solvers. The two level hierarchical solver that initiated our study was developed to solve linear system arising from hp adaptive finite element calculations, and is implemented in the PLTMG software package, version 12 [1]. This preconditioner typically requires 3-20% of the space used by the stiffness matrix for higher order elements. It has multigrid like convergence rates for a wide variety of PDEs (self-adjoint positive definite elliptic equations, convection dominated convection-diffusion equations, and highly inde nite Helmholtz equations, among others). The convergence rate is not independent of the polynomial degree p as p ! 1, but but remains strong for p 9, which is the highest polynomial degree allowed in PLTMG, due to limitations of numerical quadrature formulae. A more complete description of the method and some numerical experiments illustrating its effectiveness appear in [2]. Like traditional geometric multilevel methods, this scheme relies on extensive knowledge of the underlying finite element space in order to construct both the smoother and the coarse grid correction components.
97 MATHEMATICS AND COMPUTING↗
Final Report - Subcontract B629114
During my visits to LLNL August 20-24, 2018, and September 10-14, 2018, I worked on linear system solvers. The two level hierarchical solver that initiated our study was developed to solve linear systems arising from $hp$ adaptive finite element calculations, and is implemented in the PLTMG software package, version 13. This preconditioner typically requires 3 – 20% of the space used by the stiffness matrix for higher order elements. It has multigrid like convergence rates for a wide variety of PDEs (self-adjoint positive definite elliptic equations, convection dominated convection-diffusion equations, and highly indefinite Helmholtz equations, among others). The convergence rate is not independent of the polynomial degree $p$ as $p → ∞$, but but remains strong for $p ≤$ 9, which is the highest polynomial degree allowed in PLTMG , due to limitations of the numerical quadrature rules implemented in the software package. A more complete description of the method and some numerical experiments illustrating its effectiveness appear. Like traditional geometric multilevel methods, this scheme relies on knowledge of the underlying finite element space in order to construct the smoother and the coarse grid correction.
97 MATHEMATICS AND COMPUTING↗
Interpolative Separable Density Fitting Decomposition for Accelerating Hybrid Density Functional Calculations with Applications to Defects in Silicon
We present a new efficient way to perform hybrid density functional theory (DFT)-based electronic structure calculations. The new method uses an interpolative separable density fitting (ISDF) procedure to construct a set of numerical auxiliary basis vectors and a compact approximation of the matrix consisting of products of occupied orbitals represented in a large basis set such as the planewave basis. Such an approximation allows us to reduce the number of Poisson solves from O ($N$ $^{2}_{ϵ}$) to O ( N ϵ ) when we apply the exchange operator to occupied orbitals in an iterative method for solving the Kohn–Sham equations, where Ne is the number of electrons in the system to be studied. We show that the ISDF procedure can be carried out in O ($N$ $^{3}_{ϵ}$) operations, with a much smaller preconstant compared to methods used in existing approaches. When combined with the recently developed adaptively compressed exchange (ACE) operator formalism, which reduces the number of times the exchange operator needs to be updated, the resulting ACE-ISDF method significantly reduces the computational cost associated with the exchange operator by nearly 2 orders of magnitude compared to existing approaches for a large silicon system with 1000 atoms. We demonstrate that the ACE-ISDF method can produce accurate energies and forces for insulating and metallic systems and that it is possible to obtain converged hybrid functional calculation results for a 1000-atom bulk silicon within 10 min on 2000 computational cores. We also show that ACE-ISDF can scale to 8192 computational cores for a 4096-atom bulk silicon system. We use the ACE-ISDF method to geometrically optimize a 1000-atom silicon system with a vacancy defect using the HSE06 functional and computes its electronic structure. Here, we find that that the computed energy gap from the HSE06 functional is much closer to the experimental value compared to that produced by semilocal functionals in the DFT calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Final Report - Subcontract B623760
During my visit to LLNL during July 17{27, 2017, I worked on linear system solvers. The two level hierarchical solver that initiated our study was developed to solve linear systems arising from hp adaptive finite element calculations, and is implemented in the PLTMG software package, version 12. This preconditioner typically requires 3-20% of the space used by the stiffness matrix for higher order elements. It has multigrid like convergence rates for a wide variety of PDEs (self-adjoint positive de nite elliptic equations, convection dominated convection-diffusion equations, and highly indefinite Helmholtz equations, among others). The convergence rate is not independent of the polynomial degree p as p ! 1, but but remains strong for p 9, which is the highest polynomial degree allowed in PLTMG, due to limitations of the numerical quadrature rules implemented in the software package. A more complete description of the method and some numerical experiments illustrating its effectiveness appear in. Like traditional geometric multilevel methods, this scheme relies on knowledge of the underlying finite element space in order to construct the smoother and the coarse grid correction.
97 MATHEMATICS AND COMPUTING↗
Subcontract B635525 (Final Report)
During my visits to LLNL July 8–12 and July 22–26, 2019, I worked on linear system solvers. The two level hierarchical solver that initiated our study was developed to solve linear systems arising from $\textit{hp}$ adaptive finite element calculations, and is implemented in the $\textit{PLTMG}$ software package, version 13. This preconditioner typically requires 3–20% of the space used by the stiffness matrix for higher order elements. It has multigrid like convergence rates for a wide variety of PDEs (self-adjoint positive definite elliptic equations, convection dominated convection-diffusion equations, and highly indefinite Helmholtz equations, among others). The convergence rate is not independent of the polynomial degree $\textit{p}$ as $\textit{p} → ∞$, but remains strong for $\textit{p}$ ≤ 9, which is the highest polynomial degree allowed in $\textit{PLTMG}$, due to limitations of the numerical quadrature rules implemented in the soft- ware package. A more complete description of the method and some numerical experiments illustrating its effectiveness appear in. Like traditional geometric multilevel methods, this scheme relies on knowledge of the underlying finite element space in order to construct the smoother and the coarse grid correction.
97 MATHEMATICS AND COMPUTING↗