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At least 523 records · Page 29

Partially Collapsed Gibbs Samplers for Linear Inverse Problems and Applications to X-ray Imaging

Deblurring is one of the most common linear inverse problems in imaging, and most methods for deblurring an image assume that the convolution kernel, the so-called point spread function (PSF), is known or attempt to reconstruct the PSF simultaneously with the image. For many experimental imaging systems, like high energy X-ray radiography systems, the PSF must be computed from calibration imagery. The associated inverse problem is large-scale, so, in order to compute meaningful uncertainties with the reconstruction, it is common to use hierarchical Bayesian models and Markov chain Monte Carlo methods for sampling from the posterior. Classical Gibbs samplers can suffer from long autocorrelation lengths in the Markov chain when the reconstructed quantity in the inverse problem is finely discretized, resulting in poor computational efficiency of the Markov chain. In this work we present partially collapsed Gibbs samplers for linear inverse problems that greatly decrease correlations in the Markov chain, thus increasing the computational efficiency of the algorithms, and we present the results of the enhanced samplers on the problem of reconstructing the point spread function for an X-ray imaging system at the U.S. Department of Energy's Nevada National Security Site.

97 MATHEMATICS AND COMPUTING↗

Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics

Techniques derived from the generalized quantum master equation (GQME) framework have provided the basis for elucidating energy and charge transfer in systems ranging from molecular solids to photosynthetic complexes. Recently, the nonperturbative combination of the GQME with quantum-classical methods has resulted in approaches whose accuracy and efficiency exceed those of the original quantumclassical schemes while offering significant accuracy improvements over perturbative expansions of the GQME. In this work, we show that, while the non-Markovian memory kernel required to propagate the GQME scales quartically with the number of subsystem states, the number of trajectories required scales at most quadratically when using quantum-classical methods to construct the kernel. We then present an algorithm that allows further acceleration of the quantum-classical GQME by offering a way to selectively sample the kernel matrix elements that are most important to the process of interest. We demonstrate the utility of these advances by applying the combination of Ehrenfest mean field theory with the GQME (MF-GQME) to models of the Fenna-Matthews-Olson (FMO) complex and the light harvesting complex II (LHCII), with 7 and 14 states, respectively. This allows us to show that the MF-GQME is able to accurately capture all the relevant dynamical time scales in LHCII: the initial nonequilibrium population transfer on the femtosecond time scale, the steady state-type trapping on the picosecond time scale, and the long time population relaxation. Remarkably, all of these physical effects spanning tens of picoseconds can be encoded in a memory kernel that decays only after ~65 fs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transient anisotropic kernel for probabilistic learning on manifolds

PLoM (Probabilistic Learning on Manifolds) is a method introduced in 2016 for handling small training datasets by projecting an Itô equation from a stochastic dissipative Hamiltonian dynamical system, acting as the MCMC generator, for which the KDE-estimated probability measure with the training dataset is the invariant measure. PLoM performs a projection on a reduced-order vector basis related to the training dataset, using the diffusion maps (DMAPS) basis constructed with a time-independent isotropic kernel. In this paper, we propose a new ISDE projection vector basis built from a transient anisotropic kernel, providing an alternative to the DMAPS basis to improve statistical surrogates for stochastic manifolds with heterogeneous data. The construction ensures that for times near the initial time, the DMAPS basis coincides with the transient basis. For larger times, the differences between the two bases are characterized by the angle of their spanned vector subspaces. The optimal instant yielding the optimal transient basis is determined using an estimation of mutual information from Information Theory, which is normalized by the entropy estimation to account for the effects of the number of realizations used in the estimations. Consequently, this new vector basis better represents statistical dependencies in the learned probability measure for any dimension. Three applications with varying levels of statistical complexity and data heterogeneity validate the proposed theory, showing that the transient anisotropic kernel improves the learned probability measure.

Diffusion maps↗

Assessment of Edge-Based Viscous Method for Corner-Flow Solutions on Graphics Processing Units

A highly efficient, edge-based viscous (EBV) discretization method has been recently implemented in a practical, unstructured-grid, node-centered, finite-volume flow solver and evaluated for Reynolds-averaged Navier-Stokes (RANS) formulations. In comparison to a well-established cell-based viscous (CBV) method, the EBV method has demonstrated multifold acceleration of all viscous-kernel computations on general unstructured mixed-element grids. The viscous kernels include evaluation of viscous fluxes, diffusion terms in turbulence models, and the corresponding Jacobian terms. In this paper, an EBV implementation of a nonlinear extension of the Spalart-Allmaras turbulence model, SA-neg-QCR2000, is presented and verified. The SA-neg-QCR2000 model is used for simulating turbulent corner flows. Previously reported EBV computations have been conducted on traditional computing architectures based on central processing units (CPU). This paper assesses benefits of the EBV method on modern high-performance computing architectures based on graphics processing units (GPU). The GPU implementations of the CBV and EBV methods are verified by comparing solutions and iterative convergence with those observed in CPU computations on the same grids. A comprehensive assessment of the EBV speedup on CPU and GPU architectures is presented for established benchmark corner flows, namely, a supersonic flow through a long square duct and a subsonic flow around a NASA juncture flow model.

CFD↗

Assessment of Edge-Based Viscous Method for Corner-Flow Solutions on Graphics Processing Units

A highly efficient, edge-based viscous (EBV) discretization method has been recently implemented in a practical, unstructured-grid, node-centered, finite-volume flow solver and evaluated for Reynolds-averaged Navier-Stokes (RANS) formulations. In comparison to a well-established cell-based viscous (CBV) method, the EBV method has demonstrated multifold acceleration of all viscous-kernel computations on general unstructured mixed-element grids. The viscous kernels include evaluation of viscous fluxes, diffusion terms in turbulence models, and the corresponding Jacobian terms. In this paper, an EBV implementation of a nonlinear extension of the Spalart-Allmaras turbulence model, SA-neg-QCR2000, is presented and verified. The SA-neg-QCR2000 model is used for simulating turbulent corner flows. Previously reported EBV computations have been conducted on traditional computing architectures based on central processing units (CPU). This paper assesses benefits of the EBV method on modern high-performance computing architectures based on graphics processing units (GPU). The GPU implementations of the CBV and EBV methods are verified by comparing solutions and iterative convergence with those observed in CPU computations on the same grids. A comprehensive assessment of the EBV speedup on CPU and GPU architectures is presented for established benchmark corner flows, namely, a supersonic flow through a long square duct and a subsonic flow around a NASA juncture flow model.

CFD↗

Transient cycling of nitrogen, organic carbon and oxygen within the free-flowing Columbia River corridor: Linking exposure time dependent biogeochemical reactions to river stage fluctuations (Final project report)

The objective of this project was to develop next-generation techniques for representing the transformations of complex reaction networks like those impacting transient river-corridors, then apply them to develop upscaling tools. The project contributed significantly to the development of Lagrangian “mass transfer particle tracking” (MTPT) tools that are the first numerical framework that explicitly separates mixing and spreading processes; a crucial distinction for accurate representations of reaction rates across scales. The MTPT approach uses an operator splitting scheme where physical transport processes are simulated using classical random walk methods and each particle is treated as a “container” that carries with it any number of chemical species. Mixing between particles is simulated using a colocation-probability based mass transfer kernel and reactions are evaluated on each particle after mixing. The method is stable, accurate, and also allows the explicit modeling of residence time distributions of the individual containers of mass. The MTPT scheme allowed us to explore several research questions related to reactive transport in river corridors and complex reaction networks. We found that it is possible to quantify the exposure time distributions (ETDs) of reactants and that this does suggest some pathways to upscaling. However, comparable approximations can be obtained using simplified (reduced dimensionality) MTPT simulations in less time with similar uncertainty, so development of extensive ETD-based methods was not productive. The major findings are that i) the MTPT schemes are robust and highly accurate across a range of arbitrarily complex reactions, ii) the methods can be efficiently parallelized and the parallel performance characteristics of MTPT are predictable, and iii) the MTPT tools allow simultaneous tracking of residence time. The development of these research tools into efficient software packages continues. The methods are already available to the community because open-source, working examples have been included with all publications.

54 ENVIRONMENTAL SCIENCES↗

Extension of moment projection method to the fragmentation process

The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fission Matrix Capability for MCNP Monte Carlo

In a Monte Carlo criticality calculation, before the tallying of quantities can begin, a converged fission source (the fundamental eigenvector of the fission kernel) is required. Tallies of interest may include powers, absorption rates, leakage rates, or the multiplication factor (the fundamental eigenvalue of the fission kernel, k eff ). Just as in the power iteration method of linear algebra, if the dominance ratio (the ratio of the first and zeroth eigenvalues) is high, many iterations of neutron history simulations are required to isolate the fundamental mode of the problem. Optically large systems have large dominance ratios, and systems containing poor neutron communication between regions are also slow to converge. The fission matrix method, implemented into MCNP, addresses these problems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

SU-E-T-154: Calculation of Tissue Dose Point Kernels Using GATE Monte Carlo Simulation Toolkit to Compare with Water Dose Point Kernel

Purpose: the objective of this study was to assess utilizing water dose point kernel (DPK)instead of tissue dose point kernels in convolution algorithms.to the best of our knowledge, in providing 3D distribution of absorbed dose from a 3D distribution of the activity, the human body is considered equivalent to water. as a Result tissue variations are not considered in patient specific dosimetry. Methods: In this study Gate v7.0 was used to calculate tissue dose point kernel. the beta emitter radionuclides which have taken into consideration in this simulation include Y-90, Lu-177 and P-32 which are commonly used in nuclear medicine. the comparison has been performed for dose point kernels of adipose, bone, breast, heart, intestine, kidney, liver, lung and spleen versus water dose point kernel. Results: In order to validate the simulation the Result of 90Y DPK in water were compared with published results of Papadimitroulas et al (Med. Phys., 2012). The results represented that the mean differences between water DPK and other soft tissues DPKs range between 0.6 % and 1.96% for 90Y, except for lung and bone, where the observed discrepancies are 6.3% and 12.19% respectively. The range of DPK difference for 32P is between 1.74% for breast and 18.85% for bone. For 177Lu, the highest difference belongs to bone which is equal to 16.91%. For other soft tissues the least discrepancy is observed in kidney with 1.68%. Conclusion: In all tissues except for lung and bone, the results of GATE for dose point kernel were comparable to water dose point kernel which demonstrates the appropriateness of applying water dose point kernel instead of soft tissues in the field of nuclear medicine.

60 APPLIED LIFE SCIENCES↗

High Temperature Gas-cooled Reactor (HTGR) Graphite Pebble Fuel: Review of Technologies for Reprocessing

This report reviews literature on reprocessing high temperature gas-cooled reactor graphite fuel components. A basic review of the various fuel components used in the pebble bed type reactors is provided along with a survey of synthesis methods for the fabrication of the fuel components. Several disposal options are considered for the graphite pebble fuel elements including the storage of intact pebbles, volume reduction by separating the graphite from fuel kernels, and complete processing of the pebbles for waste storage. Existing methods for graphite removal are presented and generally consist of mechanical separation techniques such as crushing and grinding chemical techniques through the use of acid digestion and oxidation. Potential methods for reprocessing the graphite pebbles include improvements to existing methods and novel technologies that have not previously been investigated for nuclear graphite waste applications. The best overall method will be dependent on the desired final waste form and needs to factor in the technical efficiency, political concerns, cost, and implementation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

High Temperature Gas-cooled Reactor (HTGR) Graphite Pebble Fuel: Review of Technologies for Reprocessing

This report reviews literature on reprocessing high temperature gas-cooled reactor graphite fuel components. A basic review of the various fuel components used in the pebble bed type reactors is provided along with a survey of synthesis methods for the fabrication of the fuel components. Several disposal options are considered for the graphite pebble fuel elements including the storage of intact pebbles, volume reduction by separating the graphite from fuel kernels, and complete processing of the pebbles for waste storage. Existing methods for graphite removal are presented and generally consist of mechanical separation techniques such as crushing and grinding and chemical techniques through the use of acid digestion and oxidation. Potential methods for reprocessing the graphite pebbles include improvements to existing methods and novel technologies that have not previously been investigated for nuclear graphite waste applications. The best overall method will be dependent on the desired final waste form and needs to factor in the technical efficiency, political concerns, cost, and implementation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Deriving Essential Climate Variable Data from Multiple Satellite Remote Sensors Using a Consistent Fingerprinting Method

Hyperspectral observations from satellite-based sensors provide high information content for the Earth’s atmospheric and surface properties. Traditionally, long-term climate products are derived by performing spatial and temporal averaging of level-2 satellite products. It is a time-consuming process to generate level-2 data products since modern hyperspectral satellite sensors have millions of observations each day with thousands of spectral channels for each observation. Additionally, differences in level-2 retrieval algorithms can lead to errors in the climate products when fusing data from different satellite sensors. We have developed a radiometrically consistent spectral fingerprinting method, which overcomes the above-mentioned shortcomings, to derive climate change signals from multiple satellite sensors using spatiotemporally averaged level-1 data. We have applied this method to Atmospheric Infrared Sounder (AIRS) and Cross-track Infrared Sounder (CrIS) data and generated decade-long climate data records for atmospheric temperature, water vapor, cloud, trace gases, and surface skin temperature. A key component to this work is a set of observational-based radiative kernels produced from CrIS level-1 data using a single field of view (SFOV) optimal estimation retrieval algorithm. Only limited CrIS level-1 data (e.g., 1-2 years of data) are needed to the derive radiative kernels. Our Principal Component-based Radiative Model (PCRTM) enables us to perform SFOV retrievals under all sky conditions and provides radiative kernels (including those for clouds) needed by the spectral fingerprinting method. In this presentation, we will describe the basic methodology, the details of the algorithm, and results from NASA Aqua AIRS and Suomi-NPP CrIS data. The method can be applied to study future hyperspectral remote sensors such as CLARREO (Climate Absolute Radiance and Refractivity Observatory) Pathfinder (CPF), Tropospheric Emissions: Monitoring of Pollution (TEMPO), Surface Biology and Geology (SBG), Aerosol and Cloud, Convection and Precipitation (ACCP).

Xu Liu↗

A NOVEL, FULLY AUTOMATED PIPELINE FOR PERIOD ESTIMATION IN THE EROS 2 DATA SET

We present a new method to discriminate periodic from nonperiodic irregularly sampled light curves. We introduce a periodic kernel and maximize a similarity measure derived from information theory to estimate the periods and a discriminator factor. We tested the method on a data set containing 100,000 synthetic periodic and nonperiodic light curves with various periods, amplitudes, and shapes generated using a multivariate generative model. We correctly identified periodic and nonperiodic light curves with a completeness of ∼90% and a precision of ∼95%, for light curves with a signal-to-noise ratio (S/N) larger than 0.5. We characterize the efficiency and reliability of the model using these synthetic light curves and apply the method on the EROS-2 data set. A crucial consideration is the speed at which the method can be executed. Using a hierarchical search and some simplification on the parameter search, we were able to analyze 32.8 million light curves in ∼18 hr on a cluster of GPGPUs. Using the sensitivity analysis on the synthetic data set, we infer that 0.42% of the sources in the LMC and 0.61% of the sources in the SMC show periodic behavior. The training set, catalogs, and source code are all available at http://timemachine.iic.harvard.edu.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Independent calculation of dose distributions for helical tomotherapy using a conventional treatment planning system

Purpose: The dosimetric verification of treatment plans in helical tomotherapy usually is carried out via verification measurements. In this study, a method for independent dose calculation of tomotherapy treatment plans is presented, that uses a conventional treatment planning system with a pencil kernel dose calculation algorithm for generation of verification dose distributions based on patient CT data. Methods: A pencil beam algorithm that directly uses measured beam data was configured for dose calculation for a tomotherapy machine. Tomotherapy treatment plans were converted into a format readable by an in-house treatment planning system by assigning each projection to one static treatment field and shifting the calculation isocenter for each field in order to account for the couch movement. The modulation of the fluence for each projection is read out of the delivery sinogram, and with the kernel-based dose calculation, this information can directly be used for dose calculation without the need for decomposition of the sinogram. The sinogram values are only corrected for leaf output and leaf latency. Using the converted treatment plans, dose was recalculated with the independent treatment planning system. Multiple treatment plans ranging from simple static fields to real patient treatment plans were calculated using the new approach and either compared to actual measurements or the 3D dose distribution calculated by the tomotherapy treatment planning system. In addition, dose–volume histograms were calculated for the patient plans. Results: Except for minor deviations at the maximum field size, the pencil beam dose calculation for static beams agreed with measurements in a water tank within 2%/2 mm. A mean deviation to point dose measurements in the cheese phantom of 0.89% ± 0.81% was found for unmodulated helical plans. A mean voxel-based deviation of −0.67% ± 1.11% for all voxels in the respective high dose region (dose values >80%), and a mean local voxel-based deviation of −2.41% ± 0.75% for all voxels with dose values >20% were found for 11 modulated plans in the cheese phantom. Averaged over nine patient plans, the deviations amounted to −0.14% ± 1.97% (voxels >80%) and −0.95% ± 2.27% (>20%, local deviations). For a lung case, mean voxel-based deviations of more than 4% were found, while for all other patient plans, all mean voxel-based deviations were within ±2.4%. Conclusions: The presented method is suitable for independent dose calculation for helical tomotherapy within the known limitations of the pencil beam algorithm. It can serve as verification of the primary dose calculation and thereby reduce the need for time-consuming measurements. By using the patient anatomy and generating full 3D dose data, and combined with measurements of additional machine parameters, it can substantially contribute to overall patient safety.

60 APPLIED LIFE SCIENCES↗

A Method for Improving Hotspot Directional Signatures in BRDF Models Used for MODIS

The semi-empirical, kernel-driven, linear RossThick-LiSparseReciprocal (RTLSR) Bidirectional Reflectance Distribution Function (BRDF) model is used to generate the routine MODIS BRDFAlbedo product due to its global applicability and the underlying physics. A challenge of this model in regard to surface reflectance anisotropy effects comes from its underestimation of the directional reflectance signatures near the Sun illumination direction; also known as the hotspot effect. In this study, a method has been developed for improving the ability of the RTLSR model to simulate the magnitude and width of the hotspot effect. The method corrects the volumetric scattering component of the RTLSR model using an exponential approximation of a physical hotspot kernel, which recreates the hotspot magnitude and width using two free parameters (C(sub 1) and C(sub 2), respectively). The approach allows one to reconstruct, with reasonable accuracy, the hotspot effect by adjusting or using the prior values of these two hotspot variables. Our results demonstrate that: (1) significant improvements in capturing hotspot effect can be made to this method by using the inverted hotspot parameters; (2) the reciprocal nature allow this method to be more adaptive for simulating the hotspot height and width with high accuracy, especially in cases where hotspot signatures are available; and (3) while the new approach is consistent with the heritage RTLSR model inversion used to estimate intrinsic narrowband and broadband albedos, it presents some differences for vegetation clumping index (CI) retrievals. With the hotspot-related model parameters determined a priori, this method offers improved performance for various ecological remote sensing applications; including the estimation of canopy structure parameters.

airborne measurements↗

CostMAP: an open-source software package for developing cost surfaces using a multi-scale search kernel

Cost surfaces are a crucial aspect of route optimization and least cost path (LCP) calculations and are used in awide range of disciplines including computer science, landscape ecology, and energy-infrastructure modeling. Linear features introduce akey weakness to traditional routing calculations along cost surfaces because they cannot identify whether moving from acell to its adjacent neighbors constitutes crossing alinear barrier (increased cost) or following acorridor (reduced cost). Following and avoiding linear features can drastically change predicted routes. We introduce an approach to address this adjacency issue using asearch kernel that determines these critical barriers and corridors. We have built this method into anew Java-based open-source software package– CostMAP (cost surface multi-layer aggregation program)– which calculates cost surfaces and cost networks using the search kernel. CostMAP allows users to input multiple GIS data layers and to set weights and rules for developing aweighted-cost network. We compare CostMAP performance with traditional cost surface approaches and show significant performance gains– both following corridors and avoiding barriers– by modeling the movement of alarge terrestrial animal– the Baird’s Tapir (Tapirus bairdii)– in amovement ecology framework and by modeling pipeline routing for carbon capture and storage (CCS).

58 GEOSCIENCES↗

Generating Essential Climate Variables from Multiple Satellite Hyperspectral Remote Sensors

Hyperspectral observations from satellite-based sensors provide high information content for the Earth’s atmospheric and surface properties. Traditionally, long-term climate products are derived by performing spatial and temporal averaging of level-2 satellite products. There are two shortcomings of this approach. First, it is a time-consuming process to generate level-2 data products since modern hyperspectral satellite sensors have millions of observations each day with thousands of spectral channels for each observation. Secondly, differences in level-2 retrieval algorithms can lead to errors in the fused multi-satellite data. We have developed a radiometrically consistent spectral fingerprinting method, which overcomes the above-mentioned shortcomings, to derive climate change signals from multiple satellite sensors using spatiotemporally averaged level-1 data. We have applied this method to data collected from Atmospheric Infrared Sounder (AIRS) on Aqua satellite and Cross-track Infrared Sounder (CrIS) on SNPP and NOAA20 and generated decade-long climate data records for atmospheric temperature, water vapor, cloud, trace gases, and surface skin temperature. A key component to this work is a set of observational-based radiative kernels produced from CrIS level-1 data using a single field of view (SFOV) optimal estimation retrieval algorithm. Only limited CrIS level-1 data (e.g., 1-2 years of data) are needed to the derive radiative kernels. Our Principal Component-based Radiative Model (PCRTM) enables us to perform SFOV retrievals under all sky conditions and provides radiative kernels (including those for clouds) needed by the spectral fingerprinting method. In this presentation, we will describe the basic methodology, the details of the algorithm, and results from NASA Aqua AIRS and Suomi-NPP CrIS data. The method can be applied to study future hyperspectral remote sensors such as CLARREO (Climate Absolute Radiance and Refractivity Observatory) Pathfinder (CPF), Tropospheric Emissions: Monitoring of Pollution (TEMPO), Surface Biology and Geology (SBG), Atmosphere Observing System (AOS).

Xu Liu↗

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗