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Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.

Landick, Robert

Deconsolidation and Leach Burn Leach of Seven As Irradiated AGR 5/6/7 TRISO Fuel Compacts from Capsules 2, 3, 4, and 5

Seven as-irradiated Advanced Gas Reactor (AGR) 5/6/7 compacts underwent destructive post-irradiation examination via deconsolidation-leach-burn leach at Idaho National Laboratory (INL). The selection of the compacts extended the upper and lower limits of time-average volume-average (TAVA) temperature for compacts that had gone through deconsolidation-leach-burn leach so far. The measured inventories of fission products and actinides in the compact matrix and outer pyrolytic carbon were reported. Results indicated unexpectedly higher rates of fuel kernel leaching compared to compacts from AGR-1 and AGR-2. These failure rates were attributed to damage during post-irradiation sample handling, rather than irradiation itself. AGR-5/6/7 compacts have little or no matrix coverage for some particles at the top and bottom ends of cylindrical fuel compacts, making them more fragile. Sixty particles were randomly sampled from each compact, and the gamma results were reported. Three SiC shells from were identified, one of which showed signs of chemical attack in the high-irradiation temperature compact.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

AGR-5/6/7 Irradiation Test Final As-run Report

This document presents the as-run analysis of the Advanced Gas Reactor (AGR)-5/6/7 irradiation experiment. AGR-5/6/7 is the last of a series of experiments conducted in the Advanced Test Reactor (ATR) at Idaho National Laboratory in support of the development and qualification of tri-structural isotropic low-enriched fuel for use in high-temperature gas-cooled reactors. The test train contained five separate capsules that were independently controlled and monitored. Each capsule contained multiple 24.91-mm-long and 12.25-mm-dimeter compacts filled with low-enriched uranium carbide/oxide tri-structural isotropic fuel particles. The objectives of the AGR-5/6/7 experiment were to: • Irradiate reference-design fuel particles to support fuel qualification. • Establish operating margins for the fuel, beyond normal operating conditions. • Provide irradiated-fuel performance data and irradiated-fuel samples for post-irradiation examination and safety testing. The primary objective of the AGR-5/6 test (Capsules 1, 2, 4, and 5) was to verify the successful performance of the reference-design fuel under normal operating conditions. The AGR-7 test (Capsule 3) was designed to explore fuel performance at higher temperatures. Its primary objective was to demonstrate the capability of the fuel to withstand conditions beyond normal operating conditions, in support of plant design and licensing. AGR-5/6/7 will also provide irradiated-fuel performance data based on the fission gas release from particles during irradiation. To achieve the test objectives, the AGR-5/6/7 experiment was irradiated in the northeast flux trap of the ATR with a planned duration of 500 effective full-power days. The northeast flux trap was selected because its larger diameter provided greater flexibility for test-train design compared to the Large B positions used for the AGR-1 and AGR-2 irradiations, significantly enhancing test capabilities for the combined irradiation campaigns. Due to delays in the ATR schedule, the AGR-5/6/7 irradiation was significantly shorter than the originally planned 13-cycle schedule. Irradiation began on February 16, 2018 and ended on July 22, 2020, spanning nine ATR cycles (162B–168A) over two and a half years. Thus, the AGR-5/6/7 fuel compacts were irradiated for a total of approximately 360.9 effective full-power days. Final burnup values, on a per-compact basis, ranged from 5.66 to 15.26% fissions per initial heavy metal atom, while fast fluence values ranged from 1.62 to 5.55 × 1025 n/m2 (E >0.18 MeV). Time-averaged volume-averaged fuel temperatures on a capsule basis at the end of irradiation ranged from 756°C in Capsule 5 to 1313°C in Capsule 3 excluding days with significantly lower temperature during the two short powered axial locator mechanism cycles, 163A and 167A. By the end of irradiation, 48 out of 54 installed thermocouples had failed (the bottom three capsules lost all thermocouples). During the first five cycles (162B – 165A), the fission-gas isotope release-rate-to-birthrate (R/B) ratios were stable in the 10-8–10-6 range, and no in-pile particle failures were observed based on the gross gamma counts. During this time, the high exposed kernel fraction and high fuel particle temperatures in Capsule 1 led to a maximum R/B value of around 2 ? 10-6 for Kr-85m. The fission gas release in all capsules started to increase from the second half of Cycle 166A, when a large number of in-pile particle failures occurred in Capsule 1 and a gas line problem in this capsule caused fission gas leakage at various degrees into the other four capsules. This gas line problem also prevented a fission gas release measurement for Capsule 1 during the last three cycles due to gas flow isolation. By the end of irradiation, it is estimated that approximately 15 particles failed in Capsule 3, which was considered possible because the experiment was designed to operate beyond the high-temperature gas-cooled reactor normal operating temperature range. A few hundred in-pile particle failures were estimated for Capsule 1 by the end of Cycle 166A, but the total number of failures is unknown due to the lack of fission gas release data in the later cycles. Additionally, four potential in-pile failures were identified for Capsule 2 during the last cycle, Cycle 168A. In contrast, no in-pile failures were identified in the top two capsules (4 and 5) based on the absence of the typical spikes in gross gamma counts and low failure estimates using the AGR-3/4 R/B per exposed kernel model.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

AGR-5/6/7 Thermal Model with Non-uniform Gas Gaps

Fuel compact temperatures are a crucial factor in assessing the irradiation performance of tri-structural isotropic fuel particles. In the absence of direct measurement, fuel compact temperatures were calculated using a three-dimensional finite element thermal model, which is subject to simulation uncertainty. The most dominant factor in the uncertainty of calculated fuel temperatures is the gas gap uncertainty due to the nub-to-shell clearance caused by a design error of AGR-5/6/7 capsules. The thermal model was revised to examine the most probable graphite offset position for six different days during the irradiation for Capsules 1 and 2. The analysis varied the offset distance and azimuthal direction at both the top and bottom of the holder. The best-fit offset was estimated based on the minimum root mean square error of the residuals (measured minus calculated) for the operational thermocouples (TCs). From these results, the following conclusions were made: (1) The holder offsets led to slightly lower average temperatures but wider temperature variations (lower minimum and higher peak fuel temperatures) for both Capsule 1 and Capsule 2. (2) During earlier cycles (162A–164B), when numerous TCs were still operational, the best-fit offset distance varied over a specific range for both the top and bottom ([0.002–0.0035 in.] for Capsule 1 and [0.003-0.004 in] for Capsule 2). In contrast, the offset azimuthal direction varied widely, especially for the offset at the bottom of the Capsule 1 holder. This is because holder movement was somewhat constrained at the top of Capsule 1 by the TC leads running through the capsule head and into the holder and by the through tubes in Capsule 2, but the Capsule 1 bottom did not have this type of constraint. (3) During later cycles, when all TCs failed, applying the maximum possible offset of 0.006 in. to the northwest direction for both the top and bottom resulted in a calculated peak fuel temperature of 1557? in Capsule 1 (i.e., a 135? increase from 1422? with zero offset on September 20, 2019 (166A)); the maximum offset of 0.0068 in. to the south for both top and bottom resulted in a calculated peak fuel temperature of 1110°C in Capsule 2 on April 20, 2020 (i.e., a 116? increase from 994? with zero offset (168A)). High peak fuel temperatures in Capsule 1 during Cycle 166A could be the cause of massive particle failure near the end of this cycle. (4) Even though the highest temperature at the tip of Type-N TCs, such as TC-1-7, slightly exceeded 1000?, the temperature along the TC wire reached as high as 1335? assuming an offset of 0.006 in. in the northwest of Capsule 1 holder near the end of Cycle 166A. This temperature significantly exceeds the temperature threshold at which TC degradation is expected to occur, ultimately contributing to considerable particle failures in Capsule 1. For eight Type-N TCs in Capsule 2, the peak TC line temperature was much lower (i.e., 1029°C for TC-2-5), assuming maximum offset of 00068 in. to the south during cycle 168A.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

AGC-2 Graphite Preirradiation Data Analysis Report

This report describes the specimen loading order and documents all preirradiation examination material property measurement data for graphite specimens contained within the Second Advanced Graphite Capsule (AGC 2) irradiation capsule. The AGC 2 capsule is the second in six planned irradiation capsules comprising the Advanced Graphite Creep (AGC) test series. The AGC test series is used to irradiate graphite specimens in order to garner quantitative data necessary for predicting the irradiation behavior and operating performance of new nuclear grade graphites. This testing will ascertain the in service behavior of the graphite for pebble bed and prismatic very high temperature reactor designs. Similar to the First Advanced Graphite Capsule (AGC 1) preirradiation examination report, material property tests were conducted on specimens from 18 nuclear grade graphite types. However, AGC 2 tested an increased number of specimens (i.e., 512) prior to loading them into the AGC 2 irradiation assembly. All AGC 2 specimen testing was conducted at Idaho National Laboratory from July 2009 to August 2010. This report also details the specimen loading methodology for graphite specimens inside the AGC 2 irradiation capsule. The AGC 2 capsule design requires “matched pair” creep specimens that have similar dose levels above and below the neutron flux profile mid plane. This provides similar specimens with and without an applied load. Analysis in this document utilizes the neutron flux profile calculated for the AGC 2 capsule design, the capsule dimensions, and the size (i.e., length) of the selected graphite specimens to create a stacking order that produces “matched pairs” of graphite specimens above and below the AGC 2 capsule elevation mid point, thus providing specimens with similar neutron dose levels.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Fission Product Quantification and Burnup Analysis via Gamma Spectrometry of the AGR-5/6/7 TRISO Fuel Experiment

Five capsules containing varying configurations of TRISO fuel compacts were irradiated in the most recent Advanced Gas Reactor (AGR) TRISO test campaign, AGR-5/6/7. As part of the post-irradiation examination (PIE) of this work all the fuel compacts and capsule graphite holders were measured with the Precision Gamma Scanner (PGS) to determine isotopic activities and locations using gamma spectrometry. Measuring the compacts allowed for the comparison of physics model depletion calculations with the measured compact activity to validate models. These measurements also are used to find compacts of interest with low fission product retention that may be tested in subsequent PIE. Measurements of the holders can confirm fission product distribution and migration. Of the isotopes measured, Cs-137 and Cs-134 were used to estimate location of failed particles as well as determine a measured burnup estimation. Results from Capsule 1 compacts and the holder indicate many fuel particle failures occurred. There are high amounts of cesium in the holder near Stack 9 of Capsule 1 that corresponds to low fractions?measured-to-calculated (M/C) ratio?of cesium remaining in those compacts. All other capsules had cesium retention ratios near 1. The isotope 110mAg had less consistent results. Capsule 2 compacts exhibited a M/C of 0.20, much lower than anticipated for the temperatures these compacts underwent. Capsule 3 experienced much higher temperatures, >1300C and had an average M/C of 0.75. These are the opposite results than what was predicted by past AGR experiments for the relationship between temperature and isotope retention. Capsule 4 and 5 showed good fission product retention and agreement with the physics model predictions. The burnup results from the PGS measurements showed strong agreement between the physics models and the measured values. Using a ratio of Cs-134/Cs-137 to calculate the burnup match closely with the physics models. Additionally, the Cs-137 burnup results were less accurate but extremely close to the model results.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

HDG-1 Graphite Preirradiation Data Package Report

This report documents all pre-irradiation examination material-property measurement data for graphite specimens that are going to be used within the first high dose graphite (HDG) -1 irradiation capsule. The two new HDG capsules signify a major change to the AGC Experiment. HDG-1 and HDG-2 will replace the last two Advanced Graphite Creep (AGC) capsules (AGC-5 and AGC-6) which were designed to irradiate graphite at the extreme upper operational temperatures for a very-high-temperature reactor (VHTR) design, 1100°C. These very high temperature AGC-5 and AGC-6 capsules have been repurposed to re-irradiated specimens (from AGC-2, AGC-3, and AGC-4) at the lower temperatures of 600°C and 800°C. HDG-1 will be irradiated at 600°C and HDG-2 will be irradiated at 800°C. By re-irradiating the previous AGC specimens a total maximum neutron dose of around 15 dpa (displacements per atom) can be achieved for all major graphite grades at irradiation temperatures of 600°C and 800°C. Specimens in the HDG-1 capsule are made up of previously irradiated specimens from the AGC-2 capsule and unirradiated specimens prepared for the now discontinued AGC-5 capsule. Utilizing the irradiated specimens, a maximum neutron dose of around 15 dpa is anticipated. These new maximum dose levels will provide irradiated material property data over a total neutron dose range of 1-15 dpa at a temperature of 600°C when combined with the previous AGC-1 and AGC-2 irradiation data. This will provide quantitative data necessary for predicting the irradiation behavior and operating performance of new nuclear graphite grades for use within high temperature reactor designs. Similar to previous AGC test trains, HDG-1 includes the major graphite grades (IG-110, NBG-17, NBG-18, PCEA, and 2114) as well as adding the very fine-grain grade IG-430 which is of interest to the Molten Salt Reactor (MSR) designs. Also new to the HDG-1 capsule are 90 smaller geometry specimens designated as pencil specimens. These specimens take up only one third the space of a standard creep size specimen. This increased number of specimens will enhance property measurement statistics because they will provide 3 times the control specimen data at a position that would otherwise only have a single measurement.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Results of the AGR-5/6/7 UCO TRISO fuel irradiation test in the Advanced Test Reactor

AGR-5/6/7 was the last in a series of irradiation experiments sponsored by the U.S. Department of Energy in support of the development and qualification of TRISO coated particle fuel for use in a high-temperature gas-cooled reactor. This experiment was conducted to verify the performance of the reference-design TRISO-coated low-enriched UCO fuel for modular high-temperature gas-cooled reactor normal operating conditions and to explore fuel performance at temperatures substantially beyond those typical of normal operation. A total of 194 UCO fuel compacts in five capsules were irradiated in the Advanced Test Reactor for 360.9 effective full-power days, achieving final burnup ranging from 5.66% to 15.26% fissions per initial heavy metal atom and fast neutron fluence ranging from 1.62 × 10 25 to 5.55 × 10 25 n/m 2 (E > 0.18 MeV). Calculated time-averaged fuel temperatures ranged from 467 °C to 1432 °C, with a peak fuel temperature of 1536 °C. During the first five irradiation cycles (∼180 effective full-power days), 85m Kr fission gas release-rate-to-birth-rate ratios were 10 −7 –10 −6 , indicating no particle failures. Near the end of the sixth cycle, a substantial number of in-pile particle failures occurred in Capsule 1. The fission gas release from this capsule impacted the readings from the other four capsules and led to unreliable fission gas release measurements for all capsules during the last four cycles. A preliminary post-irradiation examination of Capsule 1 fuel and internal components revealed the in-pile particle failures resulted from operational issues with the capsule, not subpar performance of the fuel particles.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Water-stable direct air capture of CO 2 with microcapsules of task-specific ionic liquid and their electrothermal regeneration

Microcapsules of the task specific ionic liquid (TSIL) 1-ethyl-3-methylimidazolium 2-cyanopyrrolide [EMIM][2CNpyr] with composite polydimethylsiloxane (PDMS) shells were fabricated for use in CO 2 direct air capture (DAC) conditions. The TSIL was encapsulated using an oil-in-oil emulsion as a templating procedure through two different approaches. In the first approach, a PDMS-polyurea (PU) shell was constructed by interfacial polymerization, while in the second approach, a graphene oxide (GO)-PDMS shell was constructed by cross-linking GO sheets. The composition and structure of both capsule types were fully characterized, and their CO 2 DAC performance was evaluated by gravimetric and breakthrough analysis. Both capsules exhibited competitive capacities, with the PDMS-PU capsules and the GO-PDMS capsules reaching 0.75 mol kg −1 and 0.66 mol kg −1 , respectively. We further demonstrate that both capsule systems can be regenerated with complementary electrothermal methods. Microwave (MW) regeneration was used for the PDMS-PU capsules, effectively releasing absorbed CO 2 in less than an hour. Owing to the electrical conductivity of GO, GO-PDMS capsules were regenerated via radio frequency heating (RF). This work highlights the importance and opportunity of tuning solid–liquid composite performance for advanced applications, including direct air capture of carbon dioxide.

Al-Mahbobi, Luma [Texas A&M University, College St

Protection and enrichment: how two different carbonaceous biofilm supports improve methane yield from encapsulated anaerobic microorganisms

Encapsulating anaerobic microorganisms allows for the separation of the solids retention time from the hydraulic retention time during anaerobic wastewater treatment. The harsh chemistries involved in the process of encapsulation can have adverse effects on microorganisms for anaerobic digestion, especially methanogens, and can lead to lower methane yields after encapsulation. Improving the survival and maintaining activity of anaerobic communities during encapsulation will likely be the key to improving methane yield. In this study, we investigated the encapsulation of biomass grown as biofilms on two carbonaceous materials, biochar and powdered activated carbon (PAC), to improve methane yield. Microorganisms grown as biofilms on biochar and PAC were encapsulated in polyethylene glycol (PEG) and incubated for 10 days. After 10 days, the unamended control capsules produced 81.6 ± 5.4 μmol of methane, while PAC-amended capsules produced 129.8 ± 1.9 μmol and biochar-amended capsules produced 432.96 ± 20.8 μmol methane, with the differences being statistically significant (p < 0.05). In biochar, a higher relative abundance of methanogens led to increased methane production capacity. The ratio of the methyl coenzyme M reductase (mcrA) genes to total 16S rRNA genes in the encapsulated biochar-supported biofilms was significantly higher than that in the encapsulated unsupported (p = 4.9 × 10 −5 ) and the PAC-supported biofilms (p = 0.012). Biochar-supported biofilms also had higher methane output per mcrA or 16S rRNA gene copy number. For the PAC, biofilms were protected from ammonium persulfate (APS), a powerful oxidant used in the encapsulation process. PAC removed 92% of dissolved APS, reducing exposure of the methanogens to this chemical. Unfortunately, this removal of APS compromised capsule stability, limiting the amount of PAC that could be added to the capsules. Furthermore, amendments that improve survival and activity of methanogens should be used in the capsules instead of those that protect methanogens by interfering with encapsulant polymerization chemistry.

Resource recovery

Design of an Out-Of-Pile Experimental Facility to Demonstrate the Feasibility of In Situ Thermal Conductivity Measurements of Nuclear Fuels Under Irradiation

There is substantial merit in quantifying nuclear fuel performance under irradiation. At Oak Ridge National Laboratory (ORNL), the MiniFuel irradiation platform has become the primary test vehicle for conducting separate-effects fuel performance irradiation experiments. The MiniFuel experiment is a passively controlled capsule design deployed in the High Flux Isotope Reactor (HFIR) through which fuel performance data is collected post-irradiation. Separate effects fuels irradiation capabilities are being expanded at ORNL by developing instrumented capsule designs that aim to capture fuel performance phenomena in-situ. One such capsule will specifically target fuel specimen thermal conductivity changes as a function of fuel burnup. Due to the complexity of making this measurement on nuclear fuel in-pile, this paper describes the necessary out-of-pile testing conducted on the thermal conductivity capsule (TCC) design. The measurement is ascertained via a thermopile system with heat transferred unidirectionally through a surrogate fuel specimen sandwiched between two conductive materials. The capsules investigated in this study are representative of the in-pile design, with the primary departure from irradiation conditions being the distribution of heat generation within the capsule. In the out-of-pile experiment, an external heater was used to drive heat through the conductive slug materials and into the specimen. This paper expounds the design of the out-of-pile experimental system and the thermal conductivity measurement technique. Predictive models used to determine the sensitivity of the measurement to variables governing thermal contact conductance between the specimen and slug materials and to predict experimental results are also described. Data from the out-of-pile experiment will be used to validate the readiness of the design for insertion into HFIR for irradiation.

Parker, Trevor [ORNL]