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Contains the initial configurations and output results for the simulations reported in the paper Chemical and Morphological Structure of Transgenic Switchgrass Organosolv Lignin Extracted by Ethanol, Tetrahydrofuran, and γ-Valerolactone Pretreatments
This dataset contains the structural models for the primary transcripts of the Sphagnum divinum proteome. Additionally, for a subset of these proteins, sequence and structural alignment results are provided. This dataset represents the most thorough structural study of a Sphagnum species, also known as peat mosses, by providing three-dimensional atomic resolution structures of the majority of the encoded proteins as well as structural alignment results used in the application of annotating the proteome. References (DOI) AlphaFold v2 Monomer: https://doi.org/10.1038/s41586-021-03819-2. References (DOI) US-align2: https://doi.org/10.1038/s41592-022-01585-1
This dataset contains the structural models for the primary transcripts of the Rhodospirillum rubrum proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. rubrum proteome to those available in the AlphaFold Protein Structure Database. For proteins that have been annotated as hypothetical, sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments. References AlphaFold v2 Multimer: https://doi.org/10.1101/2021.10.04.463034. References HHBlits: https://doi.org/10.1186/s12859-019-3019-7. References SAdLSA: https://doi.org/10.3389/fbinf.2021.689960.
This dataset contains the structural models for the primary transcripts of the Desulfovibrio vulgaris proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the D. vulgaris proteome to those available in the AlphaFold Protein Structure Database (AFDB). This is a bit more complicated since the proteins reporting in the AFDB originate from an outdated form of the D. vulgaris sequence. The different versions of the D. vulgaris gene annotation are collected in the Chronology subdirectory; further consideration of these changes on the structural space of the proteome are currently underway. For proteins that have been annotated as hypothetical, sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments. References AlphaFold v2 Multimer: https://doi.org/10.1101/2021.10.04.463034. References HHblits: hhtps://doi.org/10.1186/s12859-019-3019-7. References SAdLSA: hhtps://doi.org/10.3389/fbinf.2021.689960.
This dataset contains the structural models for the primary transcripts of the Rhodopseudomonas palustris proteome. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. palustris proteome to those available in the AlphaFold Protein Structure Database.
The Sampler sequence was introduced into the SCALE nuclear modeling and simulation suite in SCALE 6.2 to perform uncertainty quantification via random sampling of nuclear data, material number densities, and dimensions. Sampler was expanded with the introduction of a parametric capability in SCALE 6.2.2. This paper discusses input for the Sampler parametric sequence and presents two case studies of analyses performed using the sequence. These case studies include preconceptual design of a package for transporting high assay low-enriched uranium (HALEU) oxide and scoping calculations to support subcritical limit development for a future update of the ANSI/ANS-8.1 (ANS-8.1) standard. The parametric capability within Sampler provides many benefits to analysts. For instance, parametric sweeps are frequently used to identify optimum parameter values as part of safety analysis or system design, but such sweeps can require substantial engineering time or may rely on custom-written scripts or scripts such as Write One, Run Many (or WORM) developed outside of any software quality assurance program. With the parametric capabilities in Sampler, however, a large number of inputs can be generated automatically without recourse to scripting by individual analysts. The parametric capability can also be used in lieu of the CSAS5S search sequence to identify optimum parameters more simply with straightforward inputs and outputs. Sampler can also be used to calculate input parameters from engineering specifications. For example, diameters can be converted to radii, or masses can be used to calculate number densities. Overall, the Sampler parametric capability provides a robust feature within SCALE, eliminating the need for user-developed scripting.
The general method for performing validation of as loaded criticality safety calculations using UNF ST&DARDS is presented in a paper by Clarity, which includes a description of the UNF-ST&DARDS system. Proof-of-principle analyses were performed in the summer of 2019 for MPC-32 dual purpose canisters (DPCs) containing pressurized water reactor (PWR) fuel assemblies. Summaries of these results are presented in this and a companion paper for this conference. The current paper describes the TSUNAMI-IP calculations performed to select applicable experiments for validation of 11 MPC-32 DPCs. The companion paper discusses the TSUNAMI-3D calculations used to generate sensitivity data to support the experiment selections discussed here. Experiment selection is based on the sensitivity/uncertainty (S/U) methods used to validate criticality safety calculations of as-loaded DPCs containing pressurized water reactor (PWR) spent nuclear fuel (SNF). This process has been demonstrated and is summarized in this paper. The approach is similar to that used in NUREG/CR-7109, which provides an approach for validation of PWR burnup credit (BUC), including major and minor actinides and major fission products. The premise of S/U-based validation is that applicable experiments—those having a similar bias to a given application system—will have similar sensitivities for each isotope and reaction in the two systems. It is assumed that cross sections with larger uncertainties are more likely to contain data errors which contribute to the bias. The integral index c k thus propagates the system sensitivities with the nuclear covariance data to calculate a correlation coefficient representing the similarity of the two systems. In this work, a c k value of 0.8 or higher is interpreted as identifying an experiment with sufficient similarity for use in validation. This paper presents a brief summary of the characteristics of the 11 MPC-32 DPCs used in the proof of-principle analysis for as-loaded criticality safety calculation validation and an overview of the critical experiment suite with which each of these DPC models was compared. A summary and discussion of c k results is also presented, followed by conclusions and a discussion of future work to be performed for validation of UNF ST&DARDS as-loaded criticality safety calculations.
The general method for performing validation of as loaded criticality safety calculations using UNF ST&DARDS is presented in a paper by Clarity, which includes a description of the UNF-ST&DARDS system. Proof-of-principle analyses were performed in the summer of 2019 for MPC-32 dual purpose canisters (DPCs) containing pressurized water reactor (PWR) fuel assemblies. Summaries of these results are presented in this and a companion paper for this conference. The current paper describes the TSUNAMI-3D calculations performed to generate sensitivity data, and the companion paper discusses the selection of critical experiments applicable for validation of the 11 MPC-32 DPCs considered. The generation of sensitivity data for as-loaded spent nuclear fuel (SNF) DPCs is a challenge given the detailed model of the fuel compositions generated by UNF ST&DARDS. Each fuel assembly is modeled with its own irradiation history in 18 axial nodes, unless the fuel assembly is damaged and thus considered as fresh by design basis. This results in a set of 576 fuel compositions, each of which must be processed separately in a multigroup (MG) calculation. Therefore, a continuous-energy (CE) TSUNAMI-3D method was chosen to alleviate this challenge. Two CE TSUNAMI-3D methods are available in SCALE 6.2.3: the iterated fission probability (IFP) and contribution-linked eigenvalue sensitivity/uncertainty estimation via track-length importance characterization (CLUTCH). Since the IFP method is not feasible because of memory requirements associated with its implementation in SCALE, the CLUTCH method was selected for these calculations. CLUTCH has been implemented in SCALE in parallel, allowing long calculations to be performed in reasonable timeframes. The two primary user inputs necessary for CLUTCH calculations are the F*(r) mesh and the number of latent generations used in determining the F*(r) function. This F*(r) function is used as the importance function for fission chains originating in a given volume element (voxel), and it is calculated using the IFP method in the skipped generations. A large number of skipped generations is thus required to ensure accurate calculation of this importance function. In these calculations, 500 generations were used to calculate the F*(r) function. For more information regarding the calculation of F*(r), see Jones [4]. The remainder of this paper is focused on the selection of the F*(r) mesh and the number of latent generations.
Kilowatt Reactor Using Stirling Technology (KRUSTY) is a prototype designed as a proof of concept for NASA’s Kilo power program, which was funded in order to create a small reactor for various space applications such as providing power for a colony on Mars or the moon and eventually as a possible option for powering rockets on deep space missions. KRUSTY was tested at the National Criticality Experiments Research Center (NCERC) located at the Nevada National Security Site (NNSS) from November 2017, through March 2018. The experimental campaign was conducted in four phases: com ponent critical experiments, cold critical experiments, warm critical runs, and high temperature demonstration. The component critical and cold critical experiments were used to determine the worth of the beryllium oxide (BeO) reflector rings and the boron carbide (B4C) control rod disks under different conditions. These conditions were altered by the addition and subtraction of other components in the assembly. The component critical phase was performed at atmospheric pressure and had four solid support rods spanning the center core; whereas the cold critical phase had the center core placed in a vacuum chamber and eight sodium-filled heat pipes spanning the center core region. This summary discusses the static neutronic analysis completed on the cold critical phase of the campaign using MCNP ® and Serpent. These two codes were used to assess any potential differences or biases in the simulation results. Understanding these potential biases is a key step toward the final goal of being able to fully analyze the transient experiments performed during phases 3 and 4 of the campaign.
A new centralized repository of high-quality MCNP models of critical benchmark experiments is currently under development at Los Alamos National Laboratory (LANL). The benchmark experiments are described in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook, and the initial set of benchmark models are derived from the Whisper Suite provided with MCNP6.2. This effort is a collaboration among the Nuclear Criticality Safety, Nuclear Data, and Monte Carlo code development/application organizations at LANL. The goal is to build a single LANL benchmark collection that is up to date with the latest ICSBEP revision, has a formal review and revision process, is contained in an open-source repository, and utilizes new Python tools for improved input and output file review. This paper describes the validation of the models associated with HEU-MET-FAST-007, “Uranium Metal Slabs Moderated with Polyethylene, Plexiglas, and Teflon”. The Monte Carlo n-Particle (MCNP) models were compared to the second revision of HEU-MET-FAST-007. The experiment considered critical configurations of highly enriched uranium (HEU) metal slabs and various moderators in 43 unique cases. The slabs of uranium were separated by layers of moderating material, forming an assembly. The assembly was separated in two halves with one half placed on a stationary table and the other attached to a moveable table that could be raised and lowered via pulleys connected to the ceiling of the shielded room. To reach criticality, the two halves were brought together with a negligible gap between the assemblies.
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In the course of re-processing the ENDF/B VIII.0 thermal scattering law data, formulas and data checking insights were developed from MCNP calculations into the neutronic characteristics of moderators. Infinite medium test calculations were carried out in MCNP as part of the verification effort for the ACE formatted thermal scattering files. Edit results from MCNP were combined with derived results to formulate several equations which give analytic insights into the neutronic behavior of moderators.
Often when planning a criticality experiment, many design configurations are iteratively investigated with a Monte Carlo transport code. The goal is that the experiment will be optimal with respect to some variable, like the fraction of fissions occurring at a certain energy range, while simultaneously being critical. Unfortunately, the Monte Carlo transport simulations are expensive, which can ultimately limit the number of configurations that can be explored. In this work, we present how Gaussian processes (GPs) can be used as a reduced-order model in a constrained Bayesian optimization (CBO) algorithm to design a criticality experiment. The GPs replace the Monte Carlo transport simulations that explore the design space. The CBO algorithm efficiently identifies new points in the design space to run the Monte Carlo transport code while respecting the criticality constraint. It does so in a manner that both improves the accuracy of the GP and finds the approximate global optimum. We demonstrate the performance of CBO with the design of a Thermal Epithermal eXperiment (TEX) for the criticality safety validation of nuclear waste models of the Hanford Tank Farm.
The TSUNAMI-1D and TSUNAMI-3D sequences for generating k eff sensitivity coefficients were first released in SCALE 5 in 2004. Several other tools were introduced in the same release, including primarily the TSUNAMI-IP code for uncertainty analysis and similarity assessments. The TSUNAMI sequences added capabilities for identifying important reactions and data for systems using sensitivity coefficients and also introduced new quantitative tools for rigorously assessing the similarity of systems. Over time, the capabilities of these tools have grown, and their use has expanded into other areas such as nuclear data assessment and nuclear covariance data testing. This paper discusses applications of the TSUNAMI tools for sensitivity calculations, sensitivity/uncertainty (S/U)-based validation, and nuclear data testing. This paper is one of a series of papers at this conference on the development and use of TSUNAMI tools. The other papers address the development of the TSUNAMI methods and the use of TSUNAMI for critical experiment design and optimization.
The new Bayesian Monte Carlo (MC) evaluation framework described in this abstract has been conceived as an attempt to improve nuclear data evaluations of differential crosssection data by removing the following two approximations conventionally employed for nuclear data evaluations: all probability density functions (PDFs) of all data and model parameters, both prior and posterior, are assumed to be normal (i.e., Gaussian) PDFs, and all uncertainties and covariances are propagated using a linear approximation. With these approximations removed, the Bayesian MC (BMC) framework could be used to account for nonlinear effects and would enable improved evaluations of differential cross sections and IBE data that are presently performed based on the assumptions itemized above. The BMC would also improve upon the uniform sampling of IBE parameters from within ranges defined by their evaluated uncertainties.
A new centralized repository of high-quality MCNP models of critical benchmark experiments is currently under development at Los Alamos National Laboratory (LANL). The repository is the combined effort of the Nuclear Criticality Safety, Nuclear Data, and Monte Carlo code development/application organizations at LANL. The initial set of benchmark models in the repository are derived from the Whisper Suite provided with MCNP6.2 and are evaluated against the benchmark experiments described in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The goal is to build a single LANL benchmark collection that is up to date with the latest ICSBEP revision, has a formal review and revision process, is contained in an open-source repository, and utilizes new Python tools for improved input and output file review. This paper describes the validation of the models associated with PU-MET-FAST-016, “Flooded 3X3X3 Arrays of 3-kg Plutonium (Pu) Metal Cylinders – Phase I”. In this critical experiment, twenty-seven 3-kg Pu metal cylinders with a height of 46.33 ± 0.15 mm and diameter of 65.25 ± 0.05 mm were arranged in a cubic array. The Pu cylinders were sealed in aluminum cans, and three cans were placed in each of nine perforated aluminum sleeves, as shown in Fig. 1. The nine sleeves were supported by an aluminum frame that allowed for control of the lateral spacing of the cylinders, both in the X and Y directions. The benchmark experiment measured thirteen configurations. Of these configurations, six were modeled using MCNP.
The SCALE 6.2.4 code package contains four sequences for calculating $k_{eff}$ sensitivity coefficients. Two of these sequences use deterministic transport solvers: a one-dimensional (1D) capability based on XSDRN, and a two-dimensional (2D) capability based on NEWT. These sequences are restricted to the multigroup (MG) treatment of neutron energy. The three-dimensional (3D) sequences use the KENO V.a or KENO-VI Monte Carlo transport codes and can be used to calculate sensitivity coefficients with either MG or continuous-energy (CE) transport. The 3D sensitivities are ultimately reported in an MG structure, regardless of the method used in the transport calculations. If desired, the sensitivity coefficients can be reported with very fine energy resolution from a CE calculation, but they are calculated only in the MG library structure in the MG mode. CE TSUNAMI methods are available in SCALE starting in SCALE version 6.2. Sensitivity coefficients were generated using the 3D sequences as part of the generation of the SCALE 6.2.2 Validation Report; difficulties encountered when using the CLUTCH method for thick, fissionable-material reflectors were discussed and investigated as documented in a previous paper. This paper discusses the difficulties encountered in generating accurate sensitivity coefficients using the CLUTCH technique for polyethylene reflectors for two fast spectrum benchmarks. Direct perturbation (DP) calculations were performed to confirm the accuracy of the total sensitivity coefficient for important isotopes with large sensitivities in the system. Discrepancies were detected for CLUTCH-calculated sensitivity coefficients in the reflector of a critical experiment with a radial polyethylene reflector. A simple polyethylene-reflected plutonium sphere was then used to further investigate the discrepancy. Calculations performed using the iterated fission probability (IFP) method generated accurate sensitivity coefficients in both cases. The results of this study emphasize the need to confirm CLUTCH sensitivity results with DP calculations. IFP calculations are generally less efficient but more reliable than CLUTCH calculations. Improvements to the CLUTCH methodology that retain the greater efficiency but address identified difficulties are therefore potentially useful to analysts.
The 2020 edition of The International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook includes a newly produced plastic-moderated evaluation, identified as PU-MET-MIXED-002 and referred to as PMM002. The 2021 edition should include another new plastic-moderated experiment, HEU-MET-THERM-004, referred to as HMT-004. These evaluations are of particular interest, as PMM-002 is moderated with polyethylene, and HMT-004 is moderated with polymethyl methacrylate (Lucite), allowing for investigation of the differences in the thermal scattering laws (TSLs) available for these materials. ENDF/B-VIII.0 includes newly produced data for 1 H-based scattering materials, including Lucite and yttrium hydride. Other available 1 H TSLs include polyethylene, light water, zirconium hydride. The unbound 1 H (free-gas) cross sections were also used. ENDF/B-VIII.0 also includes revisions made to the ENDF/B-VII.1 light water and polyethylene evaluations. Zirconium hydride was unchanged from ENDF/B-VII.1. As of this writing, there are no benchmarks included in the Verified, Archived Library of Inputs and Data (VALID) that are primarily moderated with any solid moderator, so validation that includes the PMM-002 and HMT-004 evaluations would expand the coverage to two new moderators. A study was undertaken at Oak Ridge National Laboratory with two purposes: to provide validation data based on systems that are primarily moderated with polyethylene and Lucite, and to demonstrate the reactivity changes that can result from use of different 1 H TSLs in these plastic-moderated systems. The first objective was mainly to test data and code for SCALE and AMPX, whereas the second objective was to provide useful data for practitioners on the potential variability of predicted $k_{eff}$ based on TSL changes. The use of an exactly correct TSL is often not possible given the materials involved (e.g., lubricants), but this study was intended to provide some indication of the magnitude of the changes among similar materials that can manifest through application of different TSLs in hydrogenous systems over a range of different neutron energy spectra. Unfortunately, the nominal $k_{eff}$ results exposed deviations between SCALE and Monte Carlo N-Particle (MCNP). Some of the results using different TSLs were also unexpected and difficult to explain. An investigation revealed a processing issue in AMPX that was caused by an ambiguous description of the data for incoherent elastic scattering in the ENDF manual. This issue is discussed in detail in a SCALE User Notification, and it affects some solid moderators, but it does not apply to 1 H bound in water. This issue highlights the importance of validating all TSLs used in safety analysis calculations. The remainder of this paper provides a more detailed examination of the results that triggered the investigation and a summary of the findings of that investigation.