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At least 721 records · Page 40

An ascomycete H4 variant with an unknown function

Histone variants leading to altered nucleosome structure, dynamics and DNA accessibility occur frequently, albeit rarely for H4. We carried out a comprehensive in silico scrutiny of fungal genomes, which revealed the presence of a novel H4 variant (H4E) in the ascomycetes, throughout the Pezizomycotina, in basal species of the Taphrinomycotina and also in the Glomeromycota. The coding cognate genes show a specific intron/exon organization, different from H4 canonical genes. H4Es diverge from canonical H4s mainly in the N- and C-terminal extensions, showing marked differences in the distribution and number of Lys and Arg residues, which may result in novel post-translational modifications. In Aspergillus nidulans (Pezizomycotina, Eurotiomycetes) the H4E variant protein level is low in mycelia. However, the encoding gene is well expressed at 37°C under nitrogen starvation. H4E localizes to the nucleus and interacts with H3, but its absence or overexpression does not result in any detectable phenotype. Deletion of only one of the of the two canonical H4 genes results in a strikingly impaired growth phenotype, which indicates that H4E cannot replace this canonical histone. Thus, an H4 variant is present throughout a whole subphylum of the ascomycetes, but with hitherto no experimentally detectable function.

59 BASIC BIOLOGICAL SCIENCES↗

The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle

Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. Here, we interrogated the genome-wide distribution pattern of mono- and trimethylated histone H3 lysine 4 (H3K4) using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-seq) during key phases of the Chlamydomonas cell cycle: early G 1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G 0 phase (ZT23) when they are quiescent. Tri-methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non-poly-adenylated transcripts, such as small nuclear RNAs and replication-dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono-methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP-seq data served also as a annotation tool for validation of hundreds of long non-coding RNA genes.

59 BASIC BIOLOGICAL SCIENCES↗

The Right Time at the Right Places

In my undergraduate studies at the Massachusetts Institute of Technology (MIT), the short-lived chemical physics major allowed me to evade a number of courses required for chemistry majors. Thus, it was possible to take many physics courses and most of the advanced PhD-level courses in physical chemistry. I also took the introductory electrical engineering course in computer programming. The latter allowed me to write lots of computer code as a part of my (passing, but largely unsuccessful) senior thesis directed graciously by Professor Walter Thorson. As recommended by MIT Professor John C. Slater, I moved to Stanford University with Professor Frank Harris as my PhD supervisor. Frank was the perfect advisor for me, providing very close direction during the first year, and then allowing me to develop more and more independently. Within a few days of my twenty-fifth birthday, I became an assistant professor of chemistry at the University of California, Berkeley. Eighteen years later, I moved to the University of Georgia as director of a new research institute.

autobiography↗

Design and Testing for a New Thermosyphon Irradiation Vehicle

The High Flux Isotope Reactor (HFIR) at the Oak Ridge National Laboratory (ORNL) requires most materials and all fuel experiments to be placed in a pressure containment vessel to ensure that internal contaminants such as fission products cannot be released into the primary coolant. It also requires that all experiments be capable of withstanding various accident conditions (e.g., loss of coolant) without generating vapor bubbles on the surface of the experiment in the primary coolant. These requirements are intended to artificially increase experiment temperatures by introducing a barrier between the experimental materials and the HFIR coolant, and by reducing heat loads to the HFIR primary coolant, thus ensuring that no boiling can occur. A proposed design for materials irradiation would remove these limitations by providing the required primary containment with an internal cooling flow. This would allow for experiments to be irradiated without concern for coolant contamination (e.g., from cladding failure of advanced fuel pins) or for specimen heat load. This report describes a new materials irradiation experiment design that uses a thermosyphon cooling system to allow experimental materials direct access to a liquid coolant. The new design also increases the range of conditions that can be tested in HFIR. This design will provide a unique capability to validate the performance of current and advanced fuels and materials. Because of limited supporting data for this kind of irradiation vehicle, a test program was initiated to obtain operating data that can be used to (1) qualify the vehicle for operation in HFIR and (2) validate computer models used to perform design- and safety-basis calculations. This report also describes the test facility and experimental data, and it provides a comparison of the experimental data to computer simulations. A total of 51 tests have been completed: four tests with pure steam, 12 tests with argon, and 35 tests with helium. A total of 10 tests were performed at subatmospheric pressure, and four of these were performed with pure steam. One test was conducted at a high power of 92.7 kW, six tests were HFIR startups, and two tests were HFIR loss of offsite power (LOOP). Pressures up to 10 MPa, vapor temperatures up to 583 K (310°C), and heater temperatures above 600 K (327°C) have been reached in these tests. Two computer programs, RELAP5-3D and TRACE, have been used to simulate the tests. The TRACE code has shown good agreement with the test data and has been used to model a variety of tests. This experimental facility has been very useful in demonstrating the viability of this new type of irradiation facility.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Environmental Assessment for the Above Ground Storage Capability at the Waste Isolation Pilot Plant Draft

The Waste Isolation Pilot Plant (WIPP) is the nation’s only approved repository for the disposal of defense related/defense generated transuranic (TRU) and mixed hazardous TRU waste (henceforth called TRU waste). The mission of the WIPP Project is to realize the safe disposal of TRU waste from TRU waste generator sites in the Department of Energy waste complex. The WIPP Project was authorized by Title II, Section 213(a) of Public Law 96-164 (U. S. Congress 1979). Congress designated the WIPP facility “for the express purpose of providing a research and development facility to demonstrate the safe disposal of radioactive wastes resulting from the defense activities and programs of the United States exempted from regulation by the Nuclear Regulatory Commission (NRC).” The WIPP facility is operated by the U. S. Department of Energy (DOE). Transuranic waste that is disposed in the WIPP facility is defined by Section 2(18) the WIPP Land Withdrawal Act of 1992 (LWA) (U. S. Congress, 1992) as: “waste containing more than 100 nanocuries of alpha-emitting transuranic isotopes per gram of waste, with half-lives greater than 20 years, except for: (A) high-level radioactive waste; (B) waste that the Secretary has determined, with the concurrence of the Administrator, does not need the degree of isolation required by the disposal regulations; or (C) waste that the NRC has approved for disposal on a case-by-case basis in accordance with part 61 of title 10, Code of Federal Regulations (CFR).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Inelastic analysis procedure based on the Grade 91 unified viscoplastic constitutive model for ASME implementation

This report describes a design by inelastic analysis procedure for Grade 91 to be proposed for incorporation in the ASME Boiler and Pressure Vessel Code. The package of proposed additions includes guidance on inelastic modeling and a reference constitutive model for Grade 91 to be used with the existing Section III, Division 5, Subsection HB, Subpart B rules for design by inelastic analysis. The current Code specifies acceptance criteria for design by inelastic analysis but does not provide an acceptable constitutive model for Grade 91 or any of the other Class A materials. The proposed Nonmandatory Appendix would provide such a reference model, greatly easing the use of design by inelastic analysis. As the inelastic methods produce significantly less overconservative designs than the design by elastic analysis rules this proposed Code change could reduce the design and fabrication cost of future high temperature reactors.

36 MATERIALS SCIENCE↗

Development of a multiaxial deformation measure and creep-fatigue damage summation for multiple load cycle types in support of an improved creep-fatigue design method

This report describes methods for extending the elastic perfectly plastic (EPP) simplified model test (SMT) approach to cover multiaxial load conditions and methods to combine EPP+SMT use fractions for multiple loading cycles. The completion of this work, in conjunction with companion reports on constructing and validating SMT design curves, marks the development of a complete methodology for assessing creep-fatigue damage in high temperature nuclear reactor structural components. This EPP+SMT method aims to better account for elastic follow up effects, simplify the design process, and reduce overconservatism when compared to current simplified bounding approaches in the ASME Boiler and Pressure Vessel Code Section III, Division 5, Subsection HB, Subpart B covering high temperature nuclear reactors.

36 MATERIALS SCIENCE↗

PSIP For HDF5 Pilot Project (Final Report)

Productivity and Sustainability Improvement Planning (PSIP) is a lightweight, incremental and iterative approach (much in the same spirit as Agile methodologies) for making routine software process improvements in software projects. It is designed to be easily applied in existing development workflows. Quoting from a November 2019 workshop paper describing PSIP. PSIP breaks from classic software process improvement approaches such as CMM(I), SPICE, ISO 9000 or Six Sigma, in that it trades comprehensive standards and certification-driven assessment for self-defined, internally driven goals. It does, however, carry forward such ideas as having staged models of improvement (like CMM(I)) in the form of progress tracking cards. Additionally, PSIP is more aligned with lean and agile methods; it adopts their emphasis on iterative improvement and continuous learning. At its core, PSIP is an instantiation of the Plan-Do-Check-Act management cycle (PDCA, also known as Plan-Do-Study-Adjust) which provides the foundation for much of the modern software process improvement literature. This situates PSIP within a constellation of bottom-up, inductive software process improvement methods. PSIP is designed around the notion that already overburdened teams can define and carry out a series of small, incremental steps of progression towards improvement goals without significant (there will be some, but the goal is to avoid significant) disruption to ongoing development activities. A key enabling tool in PSIP is the use of Progress Tracking Cards (PTCs) which define the steps of progression towards a given improvement goal. This is the theory of PSIP. The PSIP for HDF5 project was aimed at putting PSIP into practice with the purpose of evaluating its effectiveness in planning and facilitating quality and process improvements in a scientific software project as well as its associated artifacts. The HDF5 project was chosen as a use case to evaluate PSIP for several reasons. First, NNSA labs and LLNL in particular have a keen interest in how HDF5 quality impacts its uptake and sustainability as a community adopted and supported code. Next, HDF5 is a foundational library, a key substrate in the HPC/CSE software stack, and any improvements there realized through this contract will have benefits to many DOE applications depending on it. HDF5 also represents an older, legacy code with technical debts to pay down. These characteristics are similar to many NNSA and even some ECP code projects. But, because HDF5 is an I/O library, it represents a simpler use case within which to study PSIP than a full-fledged and significantly more complex PDE simulation code. We believe these attributes make HDF5 an ideal use case for evaluating PSIP.

97 MATHEMATICS AND COMPUTING↗

Comprehensive Margin Assessment of the ASME Section III, Division 5, Class A Primary Load Design Rules

This report provides a comprehensive margin assessment of the ASME Section III, Division 5, Subsection HB, Subpart B rules for the design of high temperature reactor components against load controlled stress limits. These rules, often called the Code primary load design rules, provide protection against creep rupture and plastic collapse under steady conditions. The method adopted here is to compare the deterministic ASME design life, according to the primary load design rules, against the expected, statistical service life of the component, considering creep rupture as the relevant failure mode. The report provides the design margin of the ASME rules in terms of the probability of premature failure -- the probability that the component fails in service before reaching the ASME design life. To complete this assessment, the report describes the development of a statistical creep life assessment procedure accounting for variations in the component loading, material creep rate, and the material rupture time. This includes a novel method for correlating creep rupture data using a Gaussian process accounting for heat-to-heat variation in the Larson-Miller time-temperature parameter. The report applies the complete margin assessment process to quantify the design margin inherent in the ASME primary load design rules as a function of temperature for relevant component geometries and materials. The overall conclusion is that the ASME rules are conservative, providing designs with very small probability of premature failure, but some optimization of the Code design rules is possible to provide a more uniform design margin.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Progress Towards International GNDS Adoption [Slides]

This presentation includes a GNDS quick overview. Libraries are increasingly available in GNDS as well as ENDF-6, Multiple evaluation / processing / checking / visualization codes have begun to support GNDS. LLNL codes FUDGE and GIDIplus are open-source tools for creating, processing and using GNDS.

Generalised Nuclear Database Structure (GNDS)↗

BUQEYE guide to projection-based emulators in nuclear physics

The BUQEYE collaboration (Bayesian Uncertainty Quantification: Errors in Your effective field theory) presents a pedagogical introduction to projection-based, reduced-order emulators for applications in low-energy nuclear physics. The term emulator refers here to a fast surrogate model capable of reliably approximating high-fidelity models. As the general tools employed by these emulators are not yet well-known in the nuclear physics community, we discuss variational and Galerkin projection methods, emphasize the benefits of offline-online decompositions, and explore how these concepts lead to emulators for bound and scattering systems that enable fast and accurate calculations using many different model parameter sets. We also point to future extensions and applications of these emulators for nuclear physics, guided by the mature field of model (order) reduction. All examples discussed here and more are available as interactive, open-source Python code so that practitioners can readily adapt projection-based emulators for their own work.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Streaming authentication and multi-level security for communications networks using quantum cryptography

Message authenticators for quantum-secured communications facilitate low-latency authentication with assurances of security. Low-latency message authenticators are especially valuable in infrastructure systems where security and latency constraints are difficult to satisfy with conventional non-quantum cryptography. For example, a message transmitter receives a message and derives an authentication tag for the message based at least in part on an authenticator that uses one or more quantum keys. The message transmitter outputs the message and its authentication tag. A message receiver receives a message and authentication tag for the message. The message receiver derives a comparison tag for the message based at least in part on an authenticator that uses one or more quantum keys. The message receiver checks whether the message is authentic based on a comparison of the authentication tag and the comparison tag. In example implementations, the authenticator uses stream-wise cyclic redundancy code operations.

97 MATHEMATICS AND COMPUTING↗

Streaming authentication and multi-level security for communications networks using quantum cryptography

Message authenticators for quantum-secured communications facilitate low-latency authentication with assurances of security. Low-latency message authenticators are especially valuable in infrastructure systems where security and latency constraints are difficult to satisfy with conventional non-quantum cryptography. For example, a message transmitter receives a message and derives an authentication tag for the message based at least in part on an authenticator that uses one or more quantum keys. The message transmitter outputs the message and its authentication tag. A message receiver receives a message and authentication tag for the message. The message receiver derives a comparison tag for the message based at least in part on an authenticator that uses one or more quantum keys. The message receiver checks whether the message is authentic based on a comparison of the authentication tag and the comparison tag. In example implementations, the authenticator uses stream-wise cyclic redundancy code operations.

Hughes, Richard J.↗

General overview of multiphysics modeling and simulation at CEA/DES/IRESNE supporting safety, operating and development of nuclear reactors and facilities

This paper presents a general overview of the innovative multiphysics research/development activities carried on by the CEA/DES/IRESNE institute. Eight main different multiphysics fields addressed by IRESNE have been listed (among others: fuel fabrication, behavior of fuels, of reactors, of corium, radionuclide transfer to environment,...) in relation with the involved coupled physics: neutron transport, fluid mechanics, electro-magnetism, heat transfer, solid mechanics and (physico-)chemistry. The major mission of IRESNE institute is to study current and future nuclear systems integrated into a low carbon energy system. To fulfill this mission, IRESNE's activities rely on the development and the implementation of multiphysics modeling, advanced coupling scheme, data transfer techniques and dedicated multiphysics experimentations. Indeed, such multiphysics simulation approach of nuclear systems is today required to deal with the complex intrinsic features of studied phenomena. This approach aims at taking into account physical phenomena interactions, at each interest modeling scale, in order to reach an accurate and predictive behavior representation of a system component or of the whole system. The final objective is to contribute to the development of digital reactor, core and fuel at CEA, by progressing on applied mathematics, high-performance computing and physical mechanism understanding.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Measuring the Dissolution of Cr and Fe at 550°-750°C in FLiNaK and FLiBe

Assessing the compatibility of 316H stainless steel with molten fluoride salts has been identified as a key research topic for molten salt reactor development. Current developers are interested in 316H stainless steel due to its ready availability and ASME code qualification. Previous studies of 316H stainless steel compatibility in molten fluoride salts have shown general agreement that Cr is selectively removed from the alloy during the exposures in molten salts. However, the extent of Cr dissolution depends on the initial purity of the salt and Fe also readily dissolves in the salt. In order to model dissolution, it is necessary to understand how time and temperature affect the dissolution rates of the alloying elements which may lead to saturation of these elements in the salt. To study the dissolution of 316H, Cr and Fe specimens were exposed in FLiNaK and LiFBeF2 (FLiBe) salt at three different temperatures (550°-750°C) and three different durations (100-2000 h) in isothermal capsule experiments.

36 MATERIALS SCIENCE↗

Assembling Multiple Models Within the RAVEN Framework

RAVEN (Risk Analysis Virtual Environment) is an INL-developed software tool that can be used to identify and increase the safety margin in complex systems. As a generic software framework, RAVEN is designed to perform parametric and probabilistic analysis based on the response of complex system codes. RAVEN is capable of investigating the system response as well as the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused toward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. RAVEN is currently able to construct multi-targets Reduced Order Models (ROMs), which are aimed to represent the response of a system (in a fixed configuration) for multiple Figures of Merits (FOMs) and time-dependent ROMs. These capabilities represent the initial steps for a larger implementation about the interaction of multiple models. In fact, in several cases, multiple models need to interface with each other since the initial conditions of one are dependent on the outcomes of another. To better understand the problem that here is solved, it is useful to consider a simple example: The following problem is considered: a weather forecast simulation code 'a' is used to compute the external (i.e. ambient) temperature in a certain location. A second model 'b' is inquired to compute the average temperature in a room having as boundary condition, among several others, the external ambient temperature. The response of the model 'b' depends on the outcome of the model 'a'. The reported example is only aimed to illustrate the reason why the creation of a framework to make interact different models is a key development for the advancement of RAVEN as a comprehensive calculation flow driver. Before reporting how the ensemble-models have been implemented, it is necessary to briefly describe the representative Model 'entities' that are available in RAVEN.

42 ENGINEERING↗

Evaluating Performance Portability with the CMS Heterogeneous Pixel Reconstruction code

In the past years the landscape of tools for expressing parallel algorithms in a portable way across various compute accelerators has continued to evolve significantly. There are many technologies on the market that provide portability between CPU, GPUs from several vendors, and in some cases even FPGAs. These technologies include C++ libraries such as Alpaka and Kokkos, compiler directives such as OpenMP, the SYCL open specification that can be implemented as a library or in a compiler, and standard C++ where the compiler is solely responsible for the offloading. Given this developing landscape, users have to choose the technology that best fits their applications and constraints. For example, in the CMS experiment the experience so far in heterogeneous reconstruction algorithms suggests that the full application contains a large number of relatively short computational kernels and memory transfer operations. In this work we use a stand-alone version of the CMS heterogeneous pixel reconstruction code as a realistic use case of HEP reconstruction software that is capable of leveraging GPUs effectively. We summarize the experience of porting this code base from CUDA to Alpaka, Kokkos, SYCL, std::par, and OpenMP offloading. We compare the event processing throughput achieved by each version on NVIDIA and AMD GPUs as well as on a CPU, and compare those to what a native version of the code achieves on each platform.

Andriotis, Nikolaos↗

BISON Simulated and Experimental Fission Product Release Comparisons from Reradiated AGR-3/4 Compacts During High Temperature Heating Tests

The fuel performance modeling code BISON was used to predict the release of fission products iodine-131 (131I), xenon-133 (133Xe), and krypton-85 (85Kr) from four re-irradiated AGR-3/4 fuel compacts containing tristructural isotropic (TRISO) coated particles during high-temperature isothermal heating tests. The AGR-3/4 fuel compacts were irradiated in the Advanced Test Reactor (ATR) as part of the third and fourth series of planned experiments to support the Advanced Gas Reactor (AGR) Program. They were subsequently stored and re-irradiated in the Neutron Radiography (NRAD) reactor for approximately five days and then stored for another five to eight days before being subjected to isothermal heating tests in the Fuel Accident Condition Simulation (FACS furnace) for 200 to 300 hours at temperatures between 1000°C and 1600°C to evaluate fission product release at elevated temperatures. New nuclide-specific fission product source term models for the three nuclides of interest were developed using the reactor multiphysics code Griffin and implemented into BISON to support this work. The new source term models were incorporated into coupled compact- and particle-scale BISON simulations, which predict spatially- and temporally-resolved radionuclide generation, radioactive decay, transport, and release throughout the entire irradiation history, including the initial ATR irradiation, NRAD re-irradiations, FACS heating tests, and intermediate periods spent in storage. The experimentally measured fission product release from the heating tests were compared to modeling release predictions calculated by BISON to evaluate how well the code compares to experimental results. Overall, the experimental measured and BISON predicted comparative release results varied but generally agreed to within 5 particle equivalents. Comparative release results identified general observations to take into consideration to help refine future models and reduce uncertainties associated with both the measurement results and predictive results. This includes developing new uranium oxycarbide (UCO) specific kernel diffusivities for the three isotopes examined to more accurately reflect the material properties of the fuel form. Deriving new diffusivities will aid in producing a more informed BISON model

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗