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At least 1,747 records · Page 97

Synchrotron‐source micro‐x‐ray computed tomography for examining butterfly eyes

Comparative anatomy is an important tool for investigating evolutionary relationships among species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations. We describe a method using synchrotron source micro-x-ray computed tomography (syn-μXCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e., butterfly and moth) eyes. Our pipeline allows for imaging at rates of ~15 min/mm 3 at 600 nm 3 resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species-independent manner thus removing any barrier to imaging any species of interest. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating diffusion and the thermodynamic factor for binary ionic mixtures

Molecular dynamics (MD) simulations are a powerful tool for the calculation of transport properties in mixtures. Not only are MD simulations capable of treating multicomponent systems, they are also applicable over a wide range of temperatures and densities. In plasma physics, this is particularly important for applications such as inertial confinement fusion. While many studies have focused on the effect of plasma coupling on transport properties, here we focus on the effects of mixing. We compute the thermodynamic factor, a measure of ideal/non-ideal mixing, for three binary ionic mixtures. Here, we consider mixtures of hydrogen and carbon, hydrogen and argon, and argon and carbon, each at 500 randomly generated state points in the warm dense matter and plasma regimes. The calculated thermodynamic factors indicate different mixing behavior across phase space, which can significantly affect the corresponding mutual diffusion coefficients. As MD simulations are still computationally expensive, we apply modern data science tools to predict the thermodynamic factor over a large phase space. Further, we propose a more accurate approximation to the mutual diffusion coefficient than the commonly applied Darken relation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Impacts of Biomass Feedstock Pre-Processing on Heat and Mass Transfer During Pyrolysis Using X-Ray Computed Tomography and Multiscale Modeling

Knowledge of the transport properties of biomass particles such as porosity, tortuosity, and permeability is paramount for high-fidelity modeling of biomass pyrolysis due to the heat and mass transfer limitations imposed by particle microstructure. X-ray computed tomography (XCT) is a non-destructive imaging method that enables full 3D reconstructions of the biomass particle microstructure with high resolution, permitting direct calculation of porosity, tortuosity, and permeability from real particle geometries. In this study, XCT imaging revealed the 3D microstructures of particles and chars from pyrolytic conversion of cylindrically cut or milled/pelletized loblolly pine samples. The porosity, tortuosity, and permeability were calculated directly from the XCT geometries via open-source microstructural analysis tool MATBOX+TauFactor (https://github.com/NREL/MATBOX_Microstructure_analysis_toolbox) and computational fluid dynamics (CFD) simulations using our solver, Mesoflow (https://github.com/NREL/mesoflow). These properties were used in a reactor scale model developed in COMSOL of the single particle reactor at NREL to investigate the impact of feedstock pre-processing on biomass conversion during pyrolysis with rigorous experimental validation.

biomass↗

Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e.g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

61 RADIATION PROTECTION AND DOSIMETRY↗

Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier through Leadership Class Computing (Final Technical Progress Report)

The performance demands on plasma-facing components (PFCs) in future fusion power plants are beyond the capability of current materials. In defining the plasma-surface interaction (PSI), it is evident that three coupled spatial regions influence PFC materials evolution and performance. These regions consist of (1) the edge and scrape-off layer region of the plasma, (2) the near-surface material response to extreme thermal and particle fluxes under the influence of, and feedback to, the plasma sheath, and (3) the structural material’s response to an intense, 14 MeV peaked neutron spectrum, which produces very high concentrations of transmuted elements through (n,p) and (n,α) reactions and structural material property degradation. The objective of this project is to develop and deploy validated, high-performance simulation tools capable of predicting the performance of tungsten-based plasma-facing components (PFCs) in a burning fusion plasma environment, which includes modeling surface morphology evolution in either erosion or re-deposition regimes, and the recycling of hydrogen species. This requires the development of a leadership-scale computational code to predict PFC behavior that is well integrated to a suite of multiscale modeling techniques to bridge the scales needed to address complex physical and computational issues at the plasma surface interface and the transition region below the surface where neutron damage processes in the bulk dominate material behavior. Successful completion of this project will provide PFC simulation tools to evaluate steady-state performance of tungsten-based PFC and divertor components in burning plasma environments. This will enable the identification of critical experiments to confirm whether practical PFC solutions exist for magnetic fusion energy beyond ITER. More specifically, the research activities within this project focus on two broadly defined research thrusts: 1) Developing a new simulation code, Xolotl-PSI to predict PFC operating lifetime and performance, that is specifically designed to take advantage of leadership class computing facilities; and 2) Integrating and applying discrete particle-based, as well as continuum-based, multiscale modeling techniques to provide scientific discovery of the mechanisms controlling PFC and bulk materials evolution under fusion plasma and 14-MeV neutron exposure; in this thrust, the challenge of scale-bridging between atomistic/microstructural modeling and the continuum-scale of PFC device performance is achieved through multiscale modeling techniques. Throughout the grant period, research at UMass Amherst focused on the atomic-scale analysis of the dynamics and kinetics (transport and reactions) of small mobile helium clusters near surfaces and grain boundaries in plasma-exposed tungsten, as well as the proper parameterization and incorporation of these processes into our SciDAC team’s continuum-level cluster dynamics code (Xolotl). Our work also included characterization of large-scale molecular-dynamics (MD) simulation results of helium implantation into tungsten based on the findings of our analysis and comparisons of Xolotl simulation predictions with the large-scale MD simulation results for Xolotl validation purposes; emphasis was placed on the impact of helium cluster dynamics/kinetics on tungsten surface morphology, near-surface tungsten structure, and helium retention. Furthermore, our work included initiation of a research program on evaluating the impact of structural defects in tungsten due to plasma exposure (such as helium nanobubbles) on tungsten’s thermophysical properties, focusing on lattice thermal conductivity. Our studies contributed to a fundamental understanding of the effects of plasma-surface interactions on the dynamical response of plasma-facing materials in nuclear fusion devices and the development of predictive hierarchical multiscale computational tools for the quantitative description of the material’s dynamical response to plasma exposure.

36 MATERIALS SCIENCE↗

Is stochastic thermodynamics the key to understanding the energy costs of computation?

The relationship between the thermodynamic and computational properties of physical systems has been a major theoretical interest since at least the 19th century. It has also become of increasing practical importance over the last half-century as the energetic cost of digital devices has exploded. Importantly, real-world computers obey multiple physical constraints on how they work, which affects their thermodynamic properties. Moreover, many of these constraints apply to both naturally occurring computers, like brains or Eukaryotic cells, and digital systems. Most obviously, all such systems must finish their computation quickly, using as few degrees of freedom as possible. This means that they operate far from thermal equilibrium. Furthermore, many computers, both digital and biological, are modular, hierarchical systems with strong constraints on the connectivity among their subsystems. Yet another example is that to simplify their design, digital computers are required to be periodic processes governed by a global clock. None of these constraints were considered in 20th-century analyses of the thermodynamics of computation. The new field of stochastic thermodynamics provides formal tools for analyzing systems subject to all of these constraints. We argue here that these tools may help us understand at a far deeper level just how the fundamental thermodynamic properties of physical systems are related to the computation they perform.

computation↗

Capturing provenance as a diagnostic tool for workflow performance evaluation and optimization

In extreme-scale computing environments such as the DOE Leadership Computing Facilities scientific workflows are routinely used to coordinate software processes for the execution of complex, computational applications that perform in-silico experiments. Monitoring the performance of workflows without also simultaneously tracking provenance is not sufficient to understand variations between runs, configurations, versions of a code, and between changes in an implemented stack, and systems, i.e. the variability of performance metrics data in their historical context. We take a provenance-based approach and demonstrate that provenance is useful as a tool for evaluating and optimizing workflow performance in extreme-scale HPC environments. We present Chimbuko, a framework for the analysis and visualization of the provenance of performance. Chimbuko implements a method for the evaluation of workflow performance from multiple components that enables the exploration of performance metrics data at scale.

97 MATHEMATICS AND COMPUTING↗

Special Issue on Data-Intensive Scalable Computing Systems

Traditional high performance computing (HPC) systems were designed from a compute-centric perspective, with an emphasis on high floating point performance. As scientific and analytics applications become more data intensive, there is a need to rethink HPC system architectures, programming models, runtime systems, and tools with a focus on scalable data intensive computing. Industry approaches supporting data intensive applications have been highly successful, leading many in the HPC community to search for ways to adapt them to HPC hardware and software contexts. Conversely, industry looks to the HPC community for their expertise in designing, deploying, and using extremely large and high performance computing systems. This special issue contains seven articles, each of which is an extended version of a paper presented in the 2015 International Workshop on Data Intensive Scalable Computing Systems (DISCS-2015) held in Austin, Texas on November 15, 2015. The workshop program included papers that ranged from programming models to systems software to storage, each with a strong focus on data intensive computing.

97 MATHEMATICS AND COMPUTING↗

Dashboard for Marine Energy Site Assessment and Monitoring

The marine energy (ME) industry presently relies upon fragmented site assessment solutions that require high resource expenditure for deployment at each site and do not leverage the wealth of readily available tools and information. A wave energy resource assessment dashboard, currently in development, will substantially improve siting, permitting, operations, and maintenance of ME projects by providing an integrated solution that is a one-stop-shop for a developer’s needs. The Site Energy Assessment and MOnitoring Dashboard (SEAMOD) will be of commercial interest to anyone seeking to deploy an ME project and is easily expandable to include tidal and wind energy site assessments. The integrated dashboard is being developed using state-of-the-art database and cloud computing methods and data-assimilative modeling tools that can be coupled with low-cost, rapidly deployable wave buoys and environmental sensing hardware. The combined software and hardware dashboard will reduce wave energy site characterization and wave climate monitoring costs by more than 60 percent and provide assessments that meet international industry standards. To realize a thriving global ME industry, the physical environment at a potential deployment site must be understood, not only for resource characterization, but also for optimization of device and power conversion performance. SEAMOD directly addresses these needs with a commercially marketable product. SEAMOD is a low-cost solution that provides comprehensive ME resource assessments, baseline environmental monitoring, and offshore characterizations required for successful ME development. The key technical objectives for Phase I were a series of software development goals, which when implemented with monitoring solutions, produced an initial proof-of-concept low-cost wave energy resources dashboard. In Phase II, the development of the prototype SEAMOD continued. The basic framework employed was the development of a revised dashboard and monitoring tool customized for ME applications by focusing on IEC site assessment and method requirements. Development was focused on the integration of full hindcast metocean products to provide hindcast resource characterization and environmental information. The final integrated dashboard provides a low-cost solution that delivers comprehensive, scalable, industry-standard energy resource assessments and offshore characterizations required for successful ME development. The integrated dashboard offers visibility of the most recent site modeling, measurements, and historical data. The application and integration of consensus-based standards for wave energy resource assessment, as determined by the International Electrotechnical Commission (IEC), are crucial for the impact and value of SEAMOD. SEAMOD includes monthly, seasonal, and yearly statistics, as well as the total 30-year record, offering temporal resolution of the IEC parameters to aid potential developers in determining the available wave energy resources in their area of interest.

16 TIDAL AND WAVE POWER↗

Generalized quantum master equations can improve the accuracy of semiclassical predictions of multitime correlation functions

Multitime quantum correlation functions are central objects in physical science, offering a direct link between the experimental observables and the dynamics of an underlying model. While experiments such as 2D spectroscopy and quantum control can now measure such quantities, the accurate simulation of such responses remains computationally expensive and sometimes impossible, depending on the system’s complexity. A natural tool to employ is the generalized quantum master equation (GQME), which can offer computational savings by extending reference dynamics at a comparatively trivial cost. However, dynamical methods that can tackle chemical systems with atomistic resolution, such as those in the semiclassical hierarchy, often suffer from poor accuracy, limiting the credence one might lend to their results. By combining work on the accuracy-boosting formulation of semiclassical memory kernels with recent work on the multitime GQME, here we show for the first time that one can exploit a multitime semiclassical GQME to dramatically improve both the accuracy of coarse mean-field Ehrenfest dynamics and obtain orders of magnitude efficiency gains.

Chemistry↗

Liquid Crystal Orientation and Shape Optimization for the Active Response of Liquid Crystal Elastomers

Liquid crystal elastomers (LCEs) are responsive materials that can undergo large reversible deformations upon exposure to external stimuli, such as electrical and thermal fields. Controlling the alignment of their liquid crystals mesogens to achieve desired shape changes unlocks a new design paradigm that is unavailable when using traditional materials. While experimental measurements can provide valuable insights into their behavior, computational analysis is essential to exploit their full potential. Accurate simulation is not, however, the end goal; rather, it is the means to achieve their optimal design. Such design optimization problems are best solved with algorithms that require gradients, i.e., sensitivities, of the cost and constraint functions with respect to the design parameters, to efficiently traverse the design space. In this work, a nonlinear LCE model and adjoint sensitivity analysis are implemented in a scalable and flexible finite element-based open source framework and integrated into a gradient-based design optimization tool. To display the versatility of the computational framework, LCE design problems that optimize both the material, i.e., liquid crystal orientation, and structural shape to reach a target actuated shapes or maximize energy absorption are solved. Multiple parameterizations, customized to address fabrication limitations, are investigated in both 2D and 3D. The case studies are followed by a discussion on the simulation and design optimization hurdles, as well as potential avenues for improving the robustness of similar computational frameworks for applications of interest.

42 ENGINEERING↗

Computational optimal transport for molecular spectra: The fully discrete case

In this study, the use of computational optimal transport is investigated as a tool for comparing two molecular spectra. Unlike other techniques for comparing molecular spectra in a pattern-recognition framework, transport distances simultaneously encode information about line positions and intensities. In addition, it is shown that transport distances are a useful alternative to Euclidean distances as Euclidean distances are based on line-by-line comparisons, while transport distances reflect broader features of molecular spectra and adequately compare spectra with different resolutions. This paper includes a tutorial on the use of optimal transport and investigates several well-chosen examples to illustrate the utility of computational optimal transport for comparing molecular spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extreme Heterogeneity 2018 - Productive Computational Science in the Era of Extreme Heterogeneity: Report for DOE ASCR Workshop on Extreme Heterogeneity

The 2018 Basic Research Needs Workshop on Extreme Heterogeneity identified five Priority Research Directions for realizing the capabilities needed to address the challenges posed in this era of rapid technological change. This report captures the outcomes of that workshop. In the context of extreme heterogeneity, it defines basic research needs and opportunities in computer science research to develop smart and trainable operating and runtime systems, programming environments, and predictive tools that will make future systems easier to adapt to scientists’ computing needs and easier for facilities to deploy securely.

97 MATHEMATICS AND COMPUTING↗

CLEAP Project: OR-SAGE Analysis for MT, UT, and CO States

The OR-SAGE tool is designed to use industry-accepted practices in screening sites and then employ the proper array of data sources through the considerable computational capabilities of GIS technology available at ORNL. The tool was developed to screen the potential for NPP siting on a national and regional basis. However, because of the tool granularity, it is often focused specifically on the immediate area around user sites of interest. If data center siting parameters can be added to OR-SAGE, the ability to evaluate data center siting on a localized scale will be beneficial.1 More than 60 data sets have been collected and processed by ORNL to develop exclusionary, avoidance, and suitability criteria for screening sites for a variety of power generation types, including nuclear power plants. Available site evaluation parameters include population density, slope, seismic activity, proximity to cooling-water sources, proximity to hazard facilities, avoidance of protected lands and floodplains, susceptibility to landslide hazards, and many others. All siting parameters should be considered as flags to inform siting decisions and should not be used to rule in or rule out any NPP site. Once data center siting parameters are identified, appropriate data sets will be collected and processed. The OR-SAGE process is very versatile. Essentially, OR-SAGE is a visual, relational database. The database partitions the contiguous United States, a total of 720 million hectares (~1.8 billion acres), into 100-m by 100-m (1 hectare or ~2.5 acre) cells. The database is tracking just under 700 million individual land cells. Successive suitability criterion is applied to each cell in the database. User-specified thresholds can be applied to each siting parameter data layer. In this manner, a variety of scenarios can be quickly and thoroughly evaluated. Data can be added and/or revised within OR-SAGE to address user interests. Siting security assessment capability is currently being added to OR-SAGE. Security is expected to be of concern at data centers whether it is collocated with a nuclear power generating technology or not. If data center is collocated with a nuclear power generating source, the security threat attractiveness level of both will likely increase. It will be of additional benefit if a potential data center site is also assessed for security vulnerability.

97 MATHEMATICS AND COMPUTING↗

End-User Evaluation of SHARP for Analysis of Sodium-Cooled Fast Reactors

The DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program is developing the SHARP toolkit to support growing reactor analysis needs in other programs. Although SHARP includes physics modules—especially the computational fluid dynamics code Nek5000 and the structural mechanics tools in Diablo—that have an existing user-base in other fields, most of the analysis and validation efforts for nuclear reactor applications have been performed by members of SHARP’s own development team. The SHARP development team includes engineers and computational scientists from a diverse set of backgrounds, including nuclear engineering. However, before the SHARP tools can be adopted by the Advanced Reactor Technology (ART) program to support the analysis of sodium-cooled fast reactors (SFRs), it would be beneficial for an outside set of analysts and engineers to begin using SHARP and providing feedback to both programs. The authors of this report were charged with learning to use SHARP, applying SHARP to SFR analyses of interest to ART, evaluating the tools, and providing a set of recommendations and requirements to guide future development efforts by the NEAMS program. The authors are engineers (nuclear, mechanical, and civil) by training; all have experience in modeling and simulation for nuclear energy applications; all have either supported ART directly or report to a supervisor who does. This report is a formal summary of the findings of this team of engineers—the potential end-users of SHARP for ART activities. In an informal way, this effort also opened up communication lines between the SHARP developers and ART engineers, which will continue beyond the scope of this effort.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Open source Modeling and optimization tools for Planning

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward to complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Simulation of the temperature distribution in the selective beam melting process for polymer material

In the present contribution the temperature distribution in the selective beam melting process for polymer materials is simulated to better understand the influence of process parameters on the properties of the produced part. The basis for the developed simulation tool is the nonlinear heat equation including temperature dependent functions for the heat capacity and the heat conduction which were obtained by experimental measurements. The effect of latent heat occurring in the process is also taken into account. The heat equation is discretized in time and space where a Runge-Kutta method of Radau IIA type is used for time integration. An adaptive finite element method is applied for the discretization in space and the model is implemented into the finite element library deal.II. The heat and cooling rate as important process parameters are simulated for different beam velocities. The ability for computing these process parameters makes the simulation tool suited for optimizing the process management of selective beam melting plants.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗