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DOE OSTI2020

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.

09 BIOMASS FUELS↗

DOE OSTI2012

Building A Universal Nuclear Energy Density Functional (UNEDF)

During the period of Dec. 1 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory. The main physics areas of UNEDF, defined at the beginning of the project, were: ab initio structure; ab initio functionals; DFT applications; DFT extensions; reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2013

Final Report for "Community Petascale Project for Accelerator Science and Simulations"

This final report describes the work that has been accomplished over the past 5 years under the Community Petascale Project for Accelerator and Simulations (ComPASS) at Tech-X Corporation. Tech-X had been involved in the full range of ComPASS activities with simulation of laser plasma accelerator concepts, mainly in collaboration with LOASIS program at LBNL, simulation of coherent electron cooling in collaboration with BNL, modeling of electron clouds in high intensity accelerators, in collaboration with researchers at Fermilab and accurate modeling of superconducting RF cavity in collaboration with Fermilab, JLab and Cockcroft Institute in the UK.

43 PARTICLE ACCELERATORS↗

DOE OSTI2013

First-principles simulation of solvation structure and deprotonation reactions of ore forming metal ions in very nonideal solutions

Advances in algorithms and computational performance achieved in this grant period have allowed the atomic level dynamical simulation of complex nanoscale materials using interparticle forces calculated directly from an accurate density functional solution to the electronic Schrödinger equation (ab-initio molecular dynamics, AIMD). Focus of this program was on the prediction and analysis of the properties of environmentally important ions in aqueous solutions. AIMD methods have provided chemical interpretations of these very complex systems with an unprecedented level of accuracy and detail. The structure of the solvation region neighboring a highly charged metal ion (e.g., 3+) in an aqueous solution is very different from that of bulk water. The many-body behaviors (polarization, charge transfer, etc.) of the ion-water and water-water interactions in this region are difficult to capture with conventional empirical potentials. However, a large numbers of waters (up to 128 waters) are required to fully describe chemical events in the extended hydrations shells and long simulation times are needed to reliably sample the system. Taken together this makes simulation at the 1 st principles level a very large computational problem. Our AIMD simulation results using these methods agree with the measured octahedral structure of the 1 st solvation shell of Al 3+ at the 1 st shell boundary and a calculated radius of 1.937 (exp. 1.9). Our calculated average 2 nd shell radius agrees remarkably well with the measured radius, 4.093 Å calculated vs. the measured value of 4.0-4.15 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Building a Universal Nuclear Energy Density Functional (UNEDF): SciDAC-2 Project

An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1, 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; and third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2012

Universal Nuclear Energy Density Functional

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

High-Fidelity Space-Time Adaptive Multiphysics Simulations in Nuclear Engineering

We delivered a series of fundamentally new computational technologies that have the potential to significantly advance the state-of-the-art of computer simulations of transient multiphysics nuclear reactor processes. These methods were implemented in the form of a C++ library, and applied to a number of multiphysics coupled problems relevant to nuclear reactor simulations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2012

Building a Universal Nuclear Energy Density Functional

During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2012

Building a Universal Nuclear Energy Density Functional (UNEDF). SciDAC-2 Project

An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. Until recently such an undertaking was hard to imagine, and even at the present time such an ambitious endeavor would be far beyond what a single researcher or a traditional research group could carry out. The UNEDF SciDAC project has developed several key computational codes and algorithms for reaching the goal of solving the nuclear quantum many-body problem throughout the chart of nuclei. Without such developments, scientific progress would not be possible. In addition the UNEDF SciDAC successfully applied these developments to solve many forefront research problems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Combined Heat and Power Systems Technology Development and Demonstration 370 kW High Efficiency Microturbine

The C370 Program was awarded in October 2010 with the ambitious goal of designing and testing the most electrically efficient recuperated microturbine engine at a rated power of less than 500 kW. The aggressive targets for electrical efficiency, emission regulatory compliance, and the estimated price point make the system state-of-the-art for microturbine engine systems. These goals will be met by designing a two stage microturbine engine identified as the low pressure spool and high pressure spool that are based on derivative hardware of Capstone’s current commercially available engines. The development and testing of the engine occurred in two phases. Phase I focused on developing a higher power and more efficient engine, that would become the low pressure spool which is based on Capstone’s C200 (200kW) engine architecture. Phase II integrated the low pressure spool created in Phase I with the high pressure spool, which is based on Capstone’s C65 (65 kW) commercially available engine. Integration of the engines, based on preliminary research, would allow the dual spool engine to provide electrical power in excess of 370 kW, with electrical efficiency approaching 42%. If both of these targets were met coupled with the overall CHP target of 85% total combined heating and electrical efficiency California Air Resources Board (CARB) level emissions, and a price target of $600 per kW, the system would represent a step change in the currently available commercial generation technology. Phase I of the C370 program required the development of the C370 low pressure spool. The goal was to increase the C200 engine power by a minimum of 25% — 250 kW — and efficiency from 32% to 37%. These increases in the C200 engine output were imperative to meet the power requirements of the engine when both spools were integrated. An additional benefit of designing and testing the C370 low pressure spool was the possibility of developing a stand-alone product for possible commercialization. The low pressure spool design activity focused on an aeropath derivative of the current C200 engine. The aeropath derivative included changes to the compressor section —compressor and inducer — and to the turbine nozzle. The increased power also necessitated a larger, more powerful generator and generator controller to support the increased power requirements. These two major design changes were completed by utilizing both advanced 3D modeling and computational fluid dynamics modelling. After design, modeling, and analysis, the decision was made to acquire and integrate the components for testing. The second task of Phase I was to integrate and test the components of the low pressure spool to validate power and efficiency. Acquisition of the components for the low pressure spool was completed utilizing Capstone’s current supplier base. Utilization of Capstone’s supply base for integration of the test article would allow — if the decision was made —expedited commercialization of the product. After integration of the engine components, the engine was tested and evaluated for performance and emissions. Test data analysis confirmed that the engine met all power and efficiency requirements and did so while maintaining CARB level emissions. The emissions were met without the use of any post processing or catalyst. After testing was completed, the DOE authorized — via a milestone review — proceeding to Phase II: the development of the integrated C370 engine. The C370 high pressure spool design activity required significant changes to the C65 engine architecture. The engine required a high power density generator, completely redesigned compressor stage, turbine section, recuperator, controls architecture, and intercooler stage asThe two most critical design challenges were the turbine section (the nozzle and turbine) and the controls architecture. The design and analysis of all of the components was completed and integrated into a system model. The system model — after numerous iterations — indicated that, once integrated, the engine will meet or exceed all system requirements. Unfortunately, the turbine section’s life requirements remain a technical challenge and will require continued refinement of the bi-metallic turbine wheel design and manufacturing approach to meet the life requirement at theses high temperatures. The current controls architecture requires substantial effort to develop a system capable of handling the high-speed, near real-time controls requirement, but it was determined not to be a technical roadblock for the project. The C370 Program has been a significant effort with state-of-the-art technical targets. The targets have pushed Capstone’s designers to the limits of current technology. The program has been fortunate to see many successes: the successful testing of the low pressure spool (C250), the development of new material processes, and the implementation of new design practices. The technology and practices learned during the program will be utilized in Capstone’s current product lines and future products. The C370 Program has been a resounding success on many fronts for the DOE and for Capstone.

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DOE OSTI2016

Printed Proliferation: The Implications of Additive Manufacturing and Nuclear Weapons Proliferation

The growth of additive manufacturing as a disruptive technology poses nuclear proliferation concerns worthy of serious consideration. Additive manufacturing began in the early 1980s with technological advances in polymer manipulation, computer capabilities, and computer-aided design (CAD) modeling. It was originally limited to rapid prototyping; however, it eventually developed into a complete means of production that has slowly penetrated the consumer market. Today, additive manufacturing machines can produce complex and unique items in a vast array of materials including plastics, metals, and ceramics. These capabilities have democratized the manufacturing industry, allowing almost anyone to produce items as simple as cup holders or as complex as jet fuel nozzles. Additive manufacturing, or three-dimensional (3D) printing as it is commonly called, relies on CAD files created or shared by individuals with additive manufacturing machines to produce a 3D object from a digital model. This sharing of files means that a 3D object can be scanned or rendered as a CAD model in one country, and then downloaded and printed in another country, allowing items to be shared globally without physically crossing borders. The sharing of CAD files online has been a challenging task for the export controls regime to manage over the years, and additive manufacturing could make these transfers more common. In this sense, additive manufacturing is a disruptive technology not only within the manufacturing industry but also within the nuclear nonproliferation world. This paper provides an overview of additive manufacturing concerns of proliferation.

3D↗

DOE OSTI2018

Low-GWP HVAC System with Ultra-small Centrifugal Compression

Mechanical Solutions, Incorporated (MSI) was awarded a contract from the United States Department of Energy under Contract DE-EE0007042 to advance the potential of vapor compression utilizing an advanced high speed centrifugal compressor with an advanced heat exchanger design. The design was mandated to maintain high efficiency while utilizing a low GWP refrigerant. The specific goal of this program was to develop an advanced 5 ton air conditioning system. The target of the air conditioner is residential and commercial. To accomplish these goals, MSI teamed with Lennox International, a leading air conditioning manufacturer. MSI would design, oversee manufacturing, assemble, and test the compressor, while Lennox designed the heat exchanger and tested the overall air conditioner. Lennox initiated the project with a detailed cycle analysis that examined systems and refrigerants. At various break points, MSI performed a preliminary compressor design to identify realizable targets. Initially, the refrigerant that was targeted was R1234ze(E), but this was subsequently rejected over concerns of flammability. R515a was ultimately accepted as a qualified fluid based upon its GWP and flammability rating. MSI performed a complete design of the centrifugal compressor based upon the cycle system design and analysis. The design was based upon advanced aerodynamics utilizing transient Computational Fluid Dynamics (CFD), as well as mechanical and rotordynamic analysis. A detailed materials investigation was conducted to ensure mechanical integrity and refrigerant compatibility. To achieve the high rotational speed required by the compressor (105,300 rpm), foil bearings were designed by MSI, as was a high speed motor to provide the required torque for the compressor. All elements of the design complied with Design for Manufacturing and Assembly (DFMA) principles. The compressor was manufactured in components, utilizing specializing subcontractors throughout the country. The components were assembled into an operational compressor in MSI’s Albany facility, where it was tested in the MSI refrigeration test loop. The compressor achieved 90% of its maximum speed during testing at MSI. The interaction between the inverter and the high speed motor was the reason that full speed could not be attained. The compressor operated smoothly and quietly at all speeds, with the bearings performing as expected. The compressor was then shipped to Lennox’s facilities in Texas, where it was tested in the entire air conditioning system. Lennox was able to achieve 95% of the maximum rotational speed. They employed the same inverter as MSI. Lennox compiled the results of the testing and based upon the results, a go forward plan has been developed to correct the issues with the inverter, as well as redesign some parts that proved to be a challenge during the program. The consensus of the team is that a fully functional air conditioning system can be developed to achieve all of the goals identified in this program.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

MC-15 Users Manual

The current iteration of field -capable neutron multiplicity counters is the Multiplicity Counter 15 tube detector (MC-15) shown in Figure 1. This was a tri-lab effort between Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and Sandia National Laboratories (SNL). The MC-15 incorporates significant improvements over previous man-portable neutron multiplicity counters of the LANL NPOD and the Ortec Fission Meter™. These improvements include finer time resolution of 100 ns, more advanced on-board computing power for near-real-time onboard analysis, a sunlight readable color touchscreen for ease of use, a USB 2.0 interface for data transfer, and hot-swappable rechargeable batteries that provide 14 hours of run time.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Modeling Astrophysical Explosions and the Nucleosynthesis of the Heavy Elements

The heavier elements in the Universe were created and dispersed in the supernova explosions of stars. These events involve a fascinating interplay of nuclear physics, gravity, hydrodynamics, neutrino and photon transport, and radioactive decay, all occurring under extreme conditions. Astronomical experiments provide a rich and constraining data set, but our theoretical understanding of supernovae remains incomplete. The goal of this project is to advance numerical models of astrophysical explosions and use them to connect the nuclear theory of supernovae to current observational and experimental programs. Our contributions focus on one important aspect of the problem --modeling the transport of radiation (both neutrino and electromagnetic) which is essential to understanding the supernova explosion mechanism, the resulting nucleosynthesis, and the observable spectra and light curves. We will exploit recent advances in high performance computing to improve 3-dimensional simulations of core collapse supernovae and neutron star mergers. The benefits include: 1) Further defining the explosive astrophysical environments that govern the nucleosynthesis of r-process nuclei. 2) Preparing the way for more realistic treatments of neutrino interactions, with the ultimate goal of making supernovae a testing ground for probing fundamental neutrino physics, e.g., unknown mixing angles and new aspects of the MSW mechanism. 3) Providing a means for testing explosion simulations and nucleosynthesis calculations against data from optical and x-ray telescopes, thereby permitting the experimental validation or falsification of supernova models. 4) Helping position nuclear physics, through the development of new algorithms of the type incorporated in our simulation codes, to play a leading role in DOE large scale computing.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Development of MGMC: A proxy Multi-Group Monte Carlo Particle Transport Application

This document details the development and current state of MGMC: a proxy Multi-Group Monte Carlo transport application. The goal of this work was to develop a light-weight Monte Carlo transport solver that could be easily reconfigured to test parallelization strategies targeting advanced architectures and heterogeneous computing environments. Additionally, MGMC is able to act as a proxy-app for testing the development of algorithms and the integration of other libraries and into Monte Carlo transport codes. MGMC is currently able to run in parallel using OpenMP for CPU threads or CUDA for NVIDIA GPUs. MGMC was also used to investigate the using SYCL for portable parallelization targeting either CPU threads, vender-agnostic GPUs, and ARM chips, detailed in Section II. In the process of developing MGMC, several other C++ libraries have been created with the intent for re-use in future research projects and potential inclusion in production-level codes, detailed in Section III. The physics capabilities in MGMC are detailed in Section IV, code verification is detailed in Section V, and performance results are detailed in Section VI.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

HPC for the EEC: Industrial Trade Tools for the Aging Energy Infrastructure

The petrochemical and refining sectors are challenged with reliably delivering safer and cleaner energy to US consumers, while meeting an ever-growing global demand. The petrochemical and refining infrastructure in the USA is aging, and corrosion and damage mechanisms are constant threats to mechanical integrity, safety, and profitability. However, governments and industry stakeholders are reluctant to replace or upgrade the existing infrastructure due to the immense cost. To better understand and mitigate the risks of aging energy infrastructure, strong technical analysis capabilities, combined with optimized monitoring and decision making, is critical. Today, this is accomplished via complex simulations and data analysis. To this end, advanced High-Performance-Computing (HPC) software will be leveraged and integrated in easy-to-use industrial trade tools, to lower the barrier for new users, increase the ease of access for experienced users, and allow for smarter decisions to be made in the midstream and downstream energy sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2016

Basic Research Needs for Innovation and Discovery of Transformative Experimental Tools

The scientific discoveries that expand the frontiers of human understanding, and that lead to the innovations of our technological world, require scientific tools and instrumentation to enable observation and manipulation of the physical world. As science advances, so too must its tools; the quest for deeper scientific insights and the drive to control chemistry and materials at the atomic and molecular levels require increasingly powerful and sophisticated instruments. A secure energy future requires technologies that use existing resources more efficiently, harness renewable resources, and efficiently store energy. The urgent demand for new energy technologies has ushered in a new era in scientific pursuit to decipher the complexity found at the core of chemical and materials processes, as articulated by the basic energy science research community in its series of Basic Research Needs (BRN) workshops. Historically, novel experimental tools and methods have been foundational in both scientific and technological advances — ranging from high-resolution microscopes that “see” atomic structures, to lithography that has enabled advances in semiconductors and computing. Today, expanding the frontiers of basic research requires new generations of instrumentation to reveal the intricacies of complex materials and chemical systems; energy systems in realistic working environments; and systems that are dynamical, far from equilibrium, and extremely heterogeneous. A concerted effort to invent, design, and build scientific instrumentation will enable new scientific breakthroughs and transformative technologies to address the most pressing energy challenges of the 21st century. To identify the highest priorities for the instrumentation innovation and development needed to address grand challenges in energy sciences, the U.S. Department of Energy’s Office of Basic Energy Sciences sponsored a workshop entitled, “Basic Research Needs for Innovation and Discovery of Transformative Experimental Tools” on June 1–3, 2016 near Washington, D.C. The workshop was attended by approximately 100 leading national and international scientific experts representing areas of basic energy sciences in chemistry, materials, physics, and biology, and included a mix of experimentalists and theorists.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗