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At least 937 records · Page 52

A Comparison of Amplitude-Based and Phase-Based Positron Emission Tomography Gating Algorithms for Segmentation of Internal Target Volumes of Tumors Subject to Respiratory Motion

Purpose: To quantitatively compare the accuracy of tumor volume segmentation in amplitude-based and phase-based respiratory gating algorithms in respiratory-correlated positron emission tomography (PET). Methods and Materials: List-mode fluorodeoxyglucose-PET data was acquired for 10 patients with a total of 12 fluorodeoxyglucose-avid tumors and 9 lymph nodes. Additionally, a phantom experiment was performed in which 4 plastic butyrate spheres with inner diameters ranging from 1 to 4 cm were imaged as they underwent 1-dimensional motion based on 2 measured patient breathing trajectories. PET list-mode data were gated into 8 bins using 2 amplitude-based (equal amplitude bins [A1] and equal counts per bin [A2]) and 2 temporal phase-based gating algorithms. Gated images were segmented using a commercially available gradient-based technique and a fixed 40% threshold of maximum uptake. Internal target volumes (ITVs) were generated by taking the union of all 8 contours per gated image. Segmented phantom ITVs were compared with their respective ground-truth ITVs, defined as the volume subtended by the tumor model positions covering 99% of breathing amplitude. Superior-inferior distances between sphere centroids in the end-inhale and end-exhale phases were also calculated. Results: Tumor ITVs from amplitude-based methods were significantly larger than those from temporal-based techniques (P=.002). For lymph nodes, A2 resulted in ITVs that were significantly larger than either of the temporal-based techniques (P<.0323). A1 produced the largest and most accurate ITVs for spheres with diameters of ≥2 cm (P=.002). No significant difference was shown between algorithms in the 1-cm sphere data set. For phantom spheres, amplitude-based methods recovered an average of 9.5% more motion displacement than temporal-based methods under regular breathing conditions and an average of 45.7% more in the presence of baseline drift (P<.001). Conclusions: Target volumes in images generated from amplitude-based gating are larger and more accurate, at levels that are potentially clinically significant, compared with those from temporal phase-based gating.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A high-order finite difference method for moving immersed domain boundaries and material interfaces

Here, we present a high-order sharp treatment of immersed moving domain boundaries and material interfaces, and apply it to the advection-diffusion equation in two and three dimensions. The spatial discretization combines dimension-split finite difference schemes with an immersed boundary treatment based on a weighted least-squares reconstruction of the solution, providing stable discretizations with up to sixth order accuracy for diffusion terms and third order accuracy for advection terms. The temporal discretization relies on a novel strategy for maintaining high-order temporal accuracy in problems with moving boundaries that minimizes implementation complexity and allows arbitrary explicit or diagonally-implicit Runge-Kutta schemes. The approach is broadly compatible with popular PDE-specialized Runge-Kutta time integrators, including low-storage, strong stability preserving, and diagonally implicit schemes. Through numerical experiments we demonstrate that the full discretization maintains high-order spatial and temporal accuracy in the presence of complex 3D geometries and for a range of boundary conditions, including Dirichlet, Neumann, and flux conditions with large jumps in coefficients.

97 MATHEMATICS AND COMPUTING↗

SmallTAL: Real-Time Egocentric Online Temporal Action Localization for the Data-Impoverished

Abstract We propose a real-time, online temporal action localization system that requires a small amount of annotated data. The main challenges we address are high intra-class variability and a large and diverse background class. We address these using a flexible frame descriptor, dynamic time warping, and a novel approach to database construction. Our solution receives egocentric RGB-D streams as input and makes predictions at regular temporal intervals. We validate our approach by localizing actions in a digital twin of an electrical substation, in which certain objects have been replaced by functional virtual replicas.

Computer Science↗

Dilute Combustion Control Using Spiking Neural Networks

Dilute combustion with exhaust gas recirculation (EGR) in spark-ignition engines presents a cost-effective method for achieving higher levels of engine efficiency. At high levels of EGR, however, cycle-to-cycle variability (CCV) of the combustion process is exacerbated by sporadic occurrences of misfires and partial burns. Previous studies have shown that temporal deterministic patterns emerge at such conditions and certain combustion cycles have a significant influence over future events. Due to the complexity of the combustion process and the nature of CCV, harnessing all the deterministic information for control purposes has remained challenging even with physics based 0-D, 1-D, and high-fidelity computational fluid dynamics (CFD) models. In this study, we present a data-driven approach to optimize the combustion process by controlling CCV adjusting the cycle-to-cycle fuel injection quantity. Readily available data from in-cylinder pressure was used to train a spiking neural network (SNN) which learns the optimal way to manage fuel injection in order to reduce CCV while maintaining acceptable levels of fuel consumption. SNNs are particularly well suited for powertrain control applications due to their ability to be deployed on FPGA-based neuromorphic hardware which are small, inexpensive, and have a low power demand. The high-performance computing (HPC) resources of Oak Ridge National Laboratory were used to run an evolutionary-based training approach for choosing the best SNN configuration that minimizes the size of the network while achieving the desired goal. The neuromorphic hardware with the optimized SNN deployed was connected to the rapid prototyping engine control system for real-time control implementation and tested on a single cylinder version of a GM LNF 4-cylinder engine. The results show a significant reduction of CCV with a small percentage of additional fuel used to stabilize the charge.

33 ADVANCED PROPULSION SYSTEMS↗

Development of Multiresolution Capabilities for the Holistic Energy Resource Optimization Network (HERON) tool A progress update

INL researchers work on technoeconomic analyses for integrated energy systems (IES) using the Framework for Optimization of ResourCes and Economics (FORCE). Within FORCE, researchers use the Holistic Energy Resource Optimization Network (HERON) tool to conduct optimization of grid portfolios under uncertain market conditions. These optimizations determine optimal capacities for all IES components and strategies for resource dispatch which maximize some economic metric (e.g., net present value). Resource dispatch occurs on finer timescales (typically hours) and thus are asked to respond to a given time series (e.g. hourly load demand profiles for a grid, or pre-determined electricity prices). Volatile and complex bidding dynamics as well as poorly forecasted weather events within deregulated markets add uncertainty to the time series; FORCE can address this uncertainty by training a reduced order model on historical time series and generate unique synthetic time series which represent individual scenarios or realizations of the market. The IES configuration can be simulated under these different sampled realizations and a stochastic optimization is conducted which optimizes the expected value of the desired economic metric. The training of a synthetic time series generator is limited by the chosen time resolution; dynamics can occur on different time scales. Seasonal demand trends can dominate faster dynamical events (such as power outages from certain sectors or severe weather events) which might not get captured correctly by the trained model. In this report, we investigate different ways of addressing the training and generation of time series on multiple time scales using three main algorithms: wavelet decomposition, dynamic mode decomposition, and generative adversarial networks for time series. We demonstrate a time series analysis that yields information on not just the frequency space but also temporal space: where a fast Fourier transform can provide what frequencies dominate, the new algorithms can provide when the frequencies dominate as well. These analyses can help improve IES optimization by allowing researchers to couple simulations at different timescales when it is most needed - seasonal, day-ahead, and real time optimization - with greater computational efficiency. Future work will include implementation of a subset of the proposed algorithms into the FORCE toolset and application of these analyses into multiple timescale optimization.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Projecting the number of new HIV infections to formulate the "Getting to Zero" strategy in Illinois, USA

Objectives: Getting to Zero (GTZ) initiatives focus on expanding use of antiretroviral treatment (ART) and pre-exposure prophylaxis (PrEP) to eliminate new HIV infections. Computational models help inform policies for implementation of ART and PrEP continuums. Such models, however, vary in their design, and may yield inconsistent predictions. Using multiple approaches can help assess the consistency in results obtained from varied modeling frameworks, and can inform optimal implementation strategies. Methods: A study using three different modeling approaches is conducted. Two approaches use statistical time series analysis techniques that incorporate temporal HIV incidence data. A third approach uses stochastic stimulation, conducted using an agent-based network model (ABNM). All three approaches are used to project HIV incidence among a key population, young Black MSM (YBMSM), over the course of the GTZ implementation period (2016-2030). Results: All three approaches suggest that simultaneously increasing PrEP and ART uptake is likely to be more effective than increasing only one, but increasing ART and PrEP by 20% points may not eliminate new HIV infections among YBMSM. The results further suggest that a 20% increase in ART is likely to be more effective than a 20% increase in PrEP. All three methods consistently project that increasing ART and PrEP by 30% simultaneously can help reach GTZ goals. Conclusions: Increasing PrEP and ART uptake by about 30% might be necessary to accomplish GTZ goals. Such scale-up may require addressing psychosocial and structural barriers to engagement in HIV and PrEP care continuums. ABNMs and other flexible modeling approaches can be extended to examine specific interventions that address these barriers and may provide important data to guide the successful intervention implementation.

60 APPLIED LIFE SCIENCES↗

Making Invisible Visible: Data-Driven Seismic Inversion With Spatio-Temporally Constrained Data Augmentation

Deep learning and data-driven approaches have shown great potential in scientific domains. The promise of data-driven techniques relies on the availability of a large volume of high-quality training datasets. Due to the high cost of obtaining data through expensive physical experiments, instruments, and simulations, data augmentation techniques for scientific applications have emerged as a new direction for obtaining scientific data recently. However, existing data augmentation techniques originating from computer vision yield physically unacceptable data samples that are not helpful for the domain problems that we are interested in. In this article, we develop new data augmentation techniques based on convolutional neural networks. Specifically, our generative models leverage different physics knowledge (such as governing equations, observable perception, and physics phenomena) to improve the quality of the synthetic data. To validate the effectiveness of our data augmentation techniques, we apply them to solve a subsurface seismic full-waveform inversion using simulated CO 2 leakage data. Our interest is to invert for subsurface velocity models associated with very small CO 2 leakage. We validate the performance of our methods using comprehensive numerical tests. Here via comparison and analysis, we show that data-driven seismic imaging can be significantly enhanced by using our data augmentation techniques. Particularly, the imaging quality has been improved by 15% in test scenarios of general-sized leakage and 17% in small-sized leakage when using an augmented training set obtained with our techniques.

58 GEOSCIENCES↗

Enhanced deep neural networks with transfer learning for distribution LMP considering load and PV uncertainties

As the flexibility of generation and demand increases in distribution systems, the residential loads are emerging as a promising means to participate in demand response and the transactive energy market. Market pricing is an instrumental mechanism for the distribution system operator to exploit the full potential of the flexible resources. The distribution locational marginal price (DLMP) can be used to guide the residential load consumption. This type of market signal helps the distribution system operator to optimize the scheduling of all resources while satisfying related network constraints through a day-ahead market. However, solving the optimization problem for large-scale systems can be computationally expensive. To address the scalability and practicability limitations of the DLMP framework, a learning-based approach is proposed in this paper to complement the day-ahead distribution market framework. Here, the proposed approach combines long short-term memory and transfer learning to develop deep neural network that can capture the spatial–temporal correlation of the input data. The model can determine the optimal DLMP for each node in a distribution system without the system parameters required to formulate the optimization problem. Testing results on IEEE 33-bus and 123-bus systems show that the proposed approach can generate a comparable DLMP against the optimization solutions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Dynamics of plasma expansion and shockwave formation in femtosecond laser-ablated aluminum plumes in argon gas at atmospheric pressures

Plasma expansion with shockwave formation during laser ablation of materials in a background gasses is a complex process. The spatial and temporal evolution of pressure, temperature, density, and velocity fields is needed for its complete understanding. We have studied the expansion of femtosecond (fs) laser-ablated aluminum (Al) plumes in Argon (Ar) gas at 0.5 and 1 atmosphere (atm). The expansion of the plume is investigated experimentally using shadowgraphy and fast-gated imaging. The computational fluid dynamics (CFD) modeling is also carried out. The position of the shock front measured by shadowgraphy and fast-gated imaging is then compared to that obtained from the CFD modeling. The results from the three methods are found to be in good agreement, especially during the initial stage of plasma expansion. The computed time- and space-resolved fields of gas-dynamic parameters have provided valuable insights into the dynamics of plasma expansion and shockwave formation in fs-pulse ablated Al plumes in Ar gas at 0.5 and 1 atm. These results are compared to our previous data on nanosecond (ns) laser ablation of Al [S. S. Harilal et al., Phys. Plasmas 19, 083504 (2012)]. It is observed that both fs and ns plumes acquire a nearly spherical shape at the end of expansion in Ar gas at 1 atm. However, due to significantly lower pulse energy of the fs laser (5 mJ) compared to pulse energy of the ns laser (100 mJ) used in our studies, the values of pressure, temperature, mass density, and velocity are found to be smaller in the fs laser plume, and their time evolution occurs much faster on the same time scale. The oscillatory shock waves clearly visible in the ns plume are not observed in the internal region of the fs plume. These experimental and computational results provide a quantitative understanding of plasma expansion and shockwave formation in fs-pulse and ns-pulse laser ablated Al plumes in an ambient gas at atmospheric pressures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spontaneous topological charging of tactoids in a living nematic

Abstract Living nematic is a realization of an active matter combining a nematic liquid crystal with swimming bacteria. The material exhibits a remarkable tendency towards spatio-temporal self-organization manifested in formation of dynamic textures of self-propelled half-integer topological defects (disclinations). Here we report on the study of such living nematic near normal inclusions, or tactoids, naturally realized in liquid crystals close to the isotropic-nematic (I–N) phase transition. On the basis of the computational analysis, we have established that tactoid’s I–N interface spontaneously acquire negative topological charge which is proportional to the tactoid’s size and depends on the concentration of bacteria. The observed negative charging is attributed to the drastic difference in the mobilities of +1/2 and −1/2 topological defects in active systems. The effect is described in the framework of a kinetic theory for point-like weakly-interacting defects with different mobilities. Our dedicated experiment fully confirmed the theoretical prediction. The results hint into new strategies for control of active matter.

59 BASIC BIOLOGICAL SCIENCES↗

Accelerated Probabilistic Marching Cubes by Deep Learning for Time-Varying Scalar Ensembles

Visualizing the uncertainty of ensemble simulations is challenging due to the large size and multivariate and temporal features of en-semble data sets. One popular approach to studying the uncertainty of ensembles is analyzing the positional uncertainty of the level sets. Probabilistic marching cubes is a technique that performs Monte Carlo sampling of multivariate Gaussian noise distributions for positional uncertainty visualization of level sets. However, the technique suffers from high computational time, making interactive visualization and analysis impossible to achieve. This paper introduces a deep-learning-based approach to learning the level-set uncertainty for two-dimensional ensemble data with a multivariate Gaussian noise assumption. We train the model using the first few time steps from time-varying ensemble data in our workflow. We demonstrate that our trained model accurately infers uncertainty in level sets for new time steps and is up to 170X faster than that of the original probabilistic model with serial computation and 10X faster than that of the original parallel computation.

Han, Mengjiao↗

Statistical Mechanics Modeling of Mesoscale Deformation in Metals

The research under this project focused on a theoretical and computational modeling of dislocation dynamics of mesoscale deformation of metal single crystals. Specifically, the work aimed to implement a continuum statistical theory of dislocations to understand strain hardening and cell structure formation under monotonic loading. These aspects of crystal deformation are manifestations of the evolution of the underlying dislocation system under mechanical loading. The project had three research tasks: 1) Investigating the statistical characteristics of dislocation systems in deformed crystals. 2) Formulating kinetic equations of dislocations and coupling these kinetics equations and crystal mechanics. 3) Computational solution of coupled crystal mechanics and dislocation kinetics. Comparison of dislocation dynamics predictions with experimental results in the area of statistical properties of dislocations and their field was also a part of the proposed effort. In the first research task, the dislocation dynamics simulation method was used to investigate the spatial, orientation, velocity, and temporal statistics of dynamical dislocation systems, and on the use of the results from this investigation to complete the kinetic description of dislocations. The second task focused on completing the formulation of a kinetic theory of dislocations that respects the discrete nature of crystallographic slip and the physics of dislocation motion and dislocation interaction in the crystal. Part of this effort also targeted the theoretical basis for establishing the connection between discrete and continuum representation of dislocations and the analysis of discrete dislocation simulation results within the continuum framework. This part of the research enables the enrichment of the kinetic description with information representing the discrete dislocation systems behavior. The third task focused on the development of physics-inspired numerical methods of solution of the coupled dislocation kinetics and crystal mechanics framework. To a large extent, this task has also been successfully started. We have developed a custom finite-element approach with mesh points being a subset of the underlying crystal structure. When used to predict the evolution of the dislocation system, the planar motion of dislocations is naturally captured for all slip systems, thus minimizing numerical errors and providing simple ways to investigate cross slip and dislocation reactions. Preliminary results in this direction show that we are closer than ever in building a predictive framework for dislocation dynamics and mesoscale plasticity based on the first principles of dislocation dynamics. The rest of the report gives and overview of the research performed under this project and highlights the key results and open questions left for future investigations.

36 MATERIALS SCIENCE↗

Mesoscale Connections Summer 2017

Our challenge derives from the fact that in metals or explosives grains, interfaces and defects control engineering performance in ways that are neither amenable to continuum codes (which fail to rigorously describe the heterogeneities derived from microstructure) nor computationally tractable to first principles atomistic calculations. This is a region called the mesoscale, which stands at the frontier of our desire to translate fundamental science insights into confidence in aging system performance over the range of extreme conditions relevant in a nuclear weapon. For dynamic problems, the phenomena of interest can require extremely good temporal resolutions. A shock wave traveling at 1000 m/s (or 1 mm/μs) passes through a grain with a diameter of 1 micron in a nanosecond (10-9 sec). Thus, to observe the mesoscale phenomena—such as dislocations or phase transformations—as the shock passes, temporal resolution better than picoseconds (10-12 sec) may be needed. As we anticipate the science challenges over the next decade, experimental insights on material performance at the micron spatial scale with picosecond temporal resolution—at the mesoscale— are a clear challenge. This is a challenge fit for Los Alamos in partnership with our sister labs and academia. Mesoscale Connections will draw attention to our progress as we tackle the mesoscale challenge. We hope you like it and encourage suggestions of content you are interested in.

36 MATERIALS SCIENCE↗

Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments

mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.

59 BASIC BIOLOGICAL SCIENCES↗

4.2.1.31 Integrated Life Cycle Sustainability Analysis

This project provides the Department of Energy's Bioenergy Technologies Office (BETO) with strategic decision-support for the evaluation of its R&D portfolio by developing, validating, and applying a coherent methodology and consistent model framework to quantify the net effects of an expanding US bioeconomy. The framework fills an analysis gap previously identified by Peer Review and supports a related milestone in BETO's Multi-Year Program Plan. The framework was scoped with inputs from practitioners in academia, national laboratories, and federal agencies. The model is a top-down, economy-wide framework using a coherent methodology to compute environmental and socio-economic metrics. It is purposefully complementary to existing bottom-up, process-based techno-economic and life cycle assessment BETO tools and uses their data as inputs. Presently, the model covers several commercial and near-commercial biofuel routes and an emerging pathway for plastics upcycling. It covers temporal detail across four time-steps and is currently being expanded with a prospective modeling capability. The model has provided analyses for the Third Triennial Report to Congress (RtC3) on the environmental impacts of the Renewable Fuel Standard (RFS2), among others. As part of this project, NREL also provides scientific support to BETO in the International Energy Agency's Technology Collaboration Program on Bioenergy (IEA Bioenergy) Task 45 on Sustainability. Here, NREL evaluates and synthesizes activities that develop, compare, or apply metrics, methods, and tools to quantify sustainability effects of bioeconomy products. NREL also coordinates related national lab involvement and a BETO Working Group on Sustainable Land Management.

bioeconomy↗

A nudged hybrid analysis and modeling approach for realtime wake-vortex transport and decay prediction

Here, we put forth a long short-term memory (LSTM) nudging framework for the enhancement of reduced order models (ROMs) of fluid flows utilizing noisy measurements for air traffic improvements. Toward emerging applications of digital twins in aviation, the proposed approach allows for constructing a realtime predictive tool for wake-vortex transport and decay systems. We build on the fact that in realistic application, there are uncertainties in initial and boundary conditions, model parameters, as well as measurements. Moreover, conventional nonlinear ROMs based on Galerkin projection (GROMs) suffer from imperfection and solution instabilities, especially for advection-dominated flows with slow decay in the Kolmogorov n-width. In the presented LSTM nudging (LSTM-N) approach, we fuse forecasts from a combination of imperfect GROM and uncertain state estimates, with sparse Eulerian sensor measurements to provide more reliable predictions in a dynamical data assimilation framework. We illustrate our concept by solving the two-dimensional vorticity transport equation. We investigate the effects of measurements noise and state estimate uncertainty on the performance of the LSTM-N behavior. We also demonstrate that it can sufficiently handle different levels of temporal and spatial measurement sparsity, and offer a huge potential in developing next-generation digital twin technologies for aerospace applications.

42 ENGINEERING↗

Using Simulation to Evaluate the Performance of Resilience Strategies and Process Failures

Fault-tolerance has been identified as a major challenge for future extreme-scale systems. Current predictions suggest that, as systems grow in size, failures will occur more frequently. Because increases in failure frequency reduce the performance and scalability of these systems, significant effort has been devoted to developing and refining resilience mechanisms to mitigate the impact of failures. However, effective evaluation of these mechanisms has been challenging. Current systems are smaller and have significantly different architectural features (e.g., interconnect, persistent storage) than we expect to see in next-generation systems. To overcome these challenges, we propose the use of simulation. Simulation has been shown to be an effective tool for investigating performance characteristics of applications on future systems. In this work, we: identify the set of system characteristics that are necessary for accurate performance prediction of resilience mechanisms for HPC systems and applications; demonstrate how these system characteristics can be incorporated into an existing large-scale simulator; and evaluate the predictive performance of our modified simulator. We also describe how we were able to optimize the simulator for large temporal and spatial scales-allowing the simulator to run 4x faster and use over 100x less memory.

97 MATHEMATICS AND COMPUTING↗

Deviational simulation of phonon transport in graphene ribbons with ab initio scattering

We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗