Assemblers: A Modular, Reconfigurable Manipulator for Autonomous in-Space Assembly
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John R Cooper↗
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A consensus-based ensemble approach to improve transcriptome assembly
Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/.
59 BASIC BIOLOGICAL SCIENCES↗
Feasibility study for detection of fuel assemblies state inside sealed dry storage casks using external gamma flux measurements - 25445
The license for the storage of spent nuclear fuel assemblies in dry casks is limited to 40 years. In Germany, a site for a final repository of spent fuel is not yet available. Therefore, this license has to be renewed for prolonged storage period. Currently, there is no experience with dry cask storage worldwide that goes beyond a period of 40 years. Beside regulatory and security aspects, there are questions concerning the long-term integrity of the spent fuel assemblies as this is of relevance for final transportation and reloading to final waste repository casks. Once the cask is filled and sealed, the knowledge about the state of the fuel assemblies is limited. This study investigates the feasibility of using external gamma flux measurements to detect the state of the spent fuel assemblies inside the cask. Monte-Carlo simulations were performed to evaluate the gamma flux distribution outside the sidewall of a cask with all intact fuel assemblies and a cask with one damaged fuel assembly, mimicking a fuel assembly with expanded rods and fuel relocation. The evaluation was performed for different location of the damaged fuel assembly and different storage times. The results of the investigation showed that the intensity and the shape of the gamma flux outside the sidewall of the cask are sufficient to identify the damaged fuel assembly, in case it is located near the inner wall of the cask. The detection of the inner damaged fuel assemblies, however, is less feasible. Due to the self-shielding of the fuel assemblies, the gamma photons which come from the inner fuel assemblies stopped within the fuel basket and assemblies materials. The gamma photons which do survive the fuel assemblies self-shielding reach the inner cask wall with not enough energy to escape the shielding of the thick cast iron wall. In general, it can be concluded that the more the damaged fuel assembly is close to the cask inner walls and that the damage is in a large scale (i.e., significant fuel relocation), the more it can be detected by external gamma flux measurements. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Autonomous Assembly of Modular Structures in Space and on Extraterrestrial Locations
The fulfillment of the new US. National Vision for Space Exploration requires many new enabling technologies to accomplish the goal of utilizing space for commercial activities and for returning humans to the moon and extraterrestrial environments. Traditionally, flight structures are manufactured as complete systems and require humans to complete the integration and assembly in orbit. These structures are bulky and require the use of heavy launch vehicles to send the units to the desired location, e.g. International Space Station (ISS). This method requires a high degree of safety, numerous space walks and significant cost for the humans to perform the assembly in orbit. For example, for assembly and maintenance of the ISS, 52 Extravehicular Activities (EVA's) have been performed so far with a total EVA time of approximately 322 hours. Sixteen (16) shuttle flights haw been to the ISS to perform these activities with an approximate cost of $450M per mission. For future space missions, costs have to be reduced to reasonably achieve the exploration goals. One concept that has been proposed is the autonomous assembly of space structures. This concept is an affordable, reliable solution to in-space and extraterrestrial assembly operations. Assembly is autonomously performed when two components containing onboard electronics join after recognizing that the joint is appropriate and in the precise position and orientation required for assembly. The mechanism only activates when the specifications are correct and m a nominal range. After assembly, local sensors and electronics monitor the integrity of the joint for feedback to a master controller. To achieve this concept will require a shift in the methods for designing space structures. In addition, innovative techniques will be required to perform the assembly autonomously. Monitoring of the assembled joint will be necessary for safety and structural integrity. If a very large structure is to be assembled in orbit, then the number of integrity sensors will be significant. Thus simple, low cost sensors are integral to the success of this concept. This paper will address these issues and will propose a novel concept for assembling space structures autonomously. The paper will present Several autonomous assembly methods. Core technologies required to achieve in space assembly will be discussed and novel techniques for communicating, sensing, docking and assembly will be detailed. These core technologies are critical to the goal of utilizing space in a cost efficient and safe manner. Finally, these technologies can also be applied to other systems both on earth and extraterrestrial environments.
Alhorn, Dean C.↗
Generation of precedence relations for mechanical assemblies
Planning of assembly sequences is essential to the manufacturing system design process. Several methodologies have been proposed to represent all the feasible assembly sequences. In this thesis, three algorithms are presented to generate three sets of precedence relations based on all the infeasible assembly tasks, all the infeasible assembly states, and all the feasible assembly sequences, respectively. The equivalence of the resulting sets of precedence relations to the AND/OR graph is established. A new property, the real time property, of a representation of assembly sequences is defined and discussed. A representation of assembly sequences is said to have the real time property, if it is possible to generate the next assembly task by testing locally in the representation, and it will guarantee that the generated assembly task will not lead the assembly sequence to a dead end situation, in which no feasible assembly task can be performed any more. It is shown that the correctness and completeness of one representation can not guarantee the real time property of the representation. It is proven that the directed graph representation and the set of precedence relations based on all the infeasible assembly states have the real time property, while the AND/OR graph representation and the set of precedence relations based on all the infeasible assembly tasks do not have the real time property. Finally in the thesis, the PLEIDEAS system, a PLanning Environment for Integrated DEsign of Assembly Systems, is described and illustrated by an example.
Zhang, Hui↗
Optimizing de novo genome assembly from PCR-amplified metagenomes
Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.
Roux, Simon↗
Optimizing de novo genome assembly from PCR-amplified metagenomes
Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.
Roux, Simon↗
Optimizing de novo genome assembly from PCR-amplified metagenomes
Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.
59 BASIC BIOLOGICAL SCIENCES↗
Self-assembly of Janus Dumbbell Nanocrystals and Their Enhanced Surface Plasmon Resonance
Self-assembly is a critical process that can greatly expand the existing structures and lead to new functionality of nanoparticle systems. Multicomponent superstructures self-assembled from nanocrystals have shown promise as multifunctional materials for various applications. Despite recent progress in assembly of homogeneous nanocrystals, synthesis and self-assembly of Janus nanocrystals with contrasting surface chemistry remains a significant challenge. Herein, we designed a novel Janus nanocrystal platform to control the self-assembly of nanoparticles in aqueous solutions by balancing the hydrophobic and hydrophilic moieties. A series of superstructures have been assembled by systematically varying the Janus balance and assembly conditions. Janus Au–Fe 3 O 4 dumbbell nanocrystals (<20 nm) were synthesized with the hydrophobic ligands coated on the Au lobe and negatively charged hydrophilic ligands coated on the Fe 3 O 4 lobe. We systematically fine-tune the lobe size ratio, surface coating, external conditions, and even additional growth of Au nanocrystal domains on the Au lobe of dumbbell nanoparticles (Au–Au–Fe 3 O 4 ) to harvest self-assembly structures including clusters, chains, vesicles, and capsules. It was discovered that in all these assemblies the hydrophobic Au lobes preferred to stay together. In addition, these superstructures clearly demonstrated different levels of enhanced surface plasmon resonance that is directly correlated with the Au coupling in the assembly structure. The strong interparticle plasmonic coupling displayed a red-shift in surface plasmon resonance, with larger structures formed by Au–Au–Fe 3 O 4 assembly extending into the near-infrared region. Self-assembly of Janus dumbbell nanocrystals can also be reversible under different pH values. In conclusion, the biphasic Janus dumbbell nanocrystals offer a platform for studying the novel interparticle coupling and open up opportunities in applications including sensing, disease diagnoses, and therapy.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Elucidating mechanisms of Photosystem I assembly and repair (Final Technical Report)
Oxygenic photosynthesis generates the carbohydrates and oxygen that support life on earth. Central to this process are photosystems I and II (PSI and PSII), large protein-pigment complexes that are among the most complex macromolecular structures in nature. Impressive advances have been made in understanding the structure and photochemical mechanisms of PSI and PSII. However, less is known about the mechanisms underlying their biogenesis. The overarching goal of this project was to elucidate mechanisms of photosystem assembly. Several proteins that are not found in mature PSI or PSII are essential for their assembly, but the assembly pathways and the role of each assembly factor are just starting to emerge. During the course of this project, we advanced understanding of this problem in several ways. First, we addressed the spatial organization of photosystem assembly by localizing many known assembly factors to specific subdomains of thylakoid membranes in plant chloroplasts. This work revealed that the "curvature" domain - the highly curved periphery of stacked granal membrane disks - is a center of photosystem assembly. However, whereas some PSI assembly factors localized exclusively to the curvature domain, another was found exclusively in granal margins and unstacked membranes. This spatial partitioning suggests an assembly line along which different assembly intermediates are physically segregated. Most assembly factors localized similarly in dark-adapted and illuminated plants, but one PSII assembly factor shifted from the curvature domain to unstacked membranes upon illumination, suggesting an unanticipated role in the repair of light-induced PSII damage. Whereas most PSII subunits were found primarily in grana stacks (as expected), one PSII subunit, PsbP, was prominent also in the curvature fraction, suggesting that PsbP has functions beyond its role in mature PSII, possibly in biogenesis or repair.
59 BASIC BIOLOGICAL SCIENCES↗
Directing Charge Transfer in Quantum Dot Assemblies
The optical and electronic properties of semiconductor quantum dots (QDs) make them attractive candidates for applications in photovoltaics, spintronics, photocatalysis, and optoelectronics. Understanding how to control the flow of charge in QD assemblies is essential for realizing novel applications. This Account explores some unique characteristics of charge transport in QD dyads, triads, and their assemblies. The emerging features of these assemblies that provide new opportunities to manipulate charge flow at the nanoscale are (1) cascading energy landscapes and band offsets to inhibit charge recombination, (2) electrostatic fields that direct charge flow through QD–QD and QD-conjugated polymer junctions, and (3) QD chirality and chiral imprinting that promotes vectorial electron and spin selective transport. Charge flow kinetics is determined by a combination of familiar electron transfer parameters (reaction free energy, reorganization energy, and electronic coupling), donor and acceptor electronic densities of states, and internal electric fields. Electron transfer and electronic structure theory, combined with kinetic modeling, place the measured kinetics of QD electron transfer donor–acceptor assemblies into a unified conceptual context. The experimental transfer rates measured in these systems depend upon structure and the internal electric fields that are present in the assemblies. A negatively charged donor and positively charged acceptor, for example, facilitates (inhibits) electron (hole) transfer, while an electric field of opposite orientation (reversal of charges) inhibits (promotes) electron (hole) transfer. These and other emerging rules that govern charge flow in NP assemblies provide a strategy to design the directionality and yield of interfacial charge transport. Chirality at the nanoscale can induce spin selective charge transport, providing new ways to direct charge (and spin) flow in QD assemblies. Magnetoresistance and magnetic conductive probe atomic force microscopy experiments show spin selective electron transport for chirally imprinted QD assemblies. Photoinduced electron transfer from achiral donor-QDs to chiral acceptor-QDs depends on the electron spin and chiroptical properties of the acceptor-QDs. These assemblies show transport characteristics that correlate with features of the QDs’ circular dichroism spectra, presenting intriguing challenges to theory, and indicating that spectroscopic signatures may assist in the design and diagnosis of functional molecular assemblies. Theoretical and experimental studies of charge transport in well-defined QD assemblies are establishing design principles for vectorial charge transport and are also refining questions surrounding the mechanism and control of these processes. Finally, these intensified efforts are forging links between fundamental discoveries regarding mechanism and practical applications for these novel assembled nanostructures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Gripper Test Assembly Status Report (FY2020)
Refueling systems for fast reactors are designed to handle fresh and used core assemblies (fuel, reflector, and shield core assemblies) within the reactor vessel in an opaque coolant environment without visual reference. These refueling machines are designed to work in a sodium (or other fast reactor coolant) and argon vapor space environment and are engineered with the rotatable plug system to allow for the movement of fresh and spent fuel into and out of the reactor core. The refueling machines are a critical component in any reactor and thus need to undergo extensive testing in a prototypic environment to ensure that they will meet all of the system functions and requirements. Argonne has developed an innovative compact refueling system design for the Advanced Fast Reactor-100 that is based upon some mechanisms used in previous reactor designs, such as the U.K.’s Prototype Fast Reactor (PFR) and some mechanisms that have not been used in sodium. This compact refueling machine supports the reduction in size of the AFR-100’s reactor vessel, and if fully developed, would support and inform the development of the in-vessel refueling machines for such commercial reactors as the GEH PRISM reactor plant, the ARC Clean Energy’s ARC-100 reactor, and the Natrium reactor, among others. This refueling system is a vital component of a fast reactor that supports reducing the cost of the reactor and increasing its reliability. During the development of the compact fuel handling machine conceptual design for the AFR-100, a lack of testing data for many mechanical components in sodium under typical in-reactor loads and conditions was discovered. The reduction in lifetime of the various mechanical components in the liquid sodium environment needs to be quantified versus the calculated component lifetimes under normal conditions in the testing while they are subjected to typical loading profiles experienced in the past. The Gripper Test Assembly discussed here includes a full-size gripper device with appropriate mechanical features that will be tested in sodium to provide this testing data. The Gripper Test Assembly is used to test various mechanical fuel handling components submerged in high temperature liquid sodium. These mechanisms are gears, bearings, gripper jaws and head, universal joints and shafts, ball screws, among others. These components will be tested under the typical sodium environmental conditions experienced during refueling operations with appropriate loading conditions that simulate the removal and insertion of core assemblies into a fast reactor grid plate structure. This Gripper Test Assembly is the second in a series of refueling system mechanisms developed for testing in sodium. The first test assembly is the Gear Test Assembly (GTA) which was used to test the performance of gears and bearings operating in sodium. Because of the successful testing conducted with the GTA, it was decided to continue with the development of the Gripper Test Assembly which uses the same gears and bearings tested in GTA. Using the data collected during operation of this gripper test assembly, lifetime reduction factors of the various mechanical components can be calculated for the material combinations selected. These lifetime reduction factors can be used in the design of future mechanical systems which operate in these environments to accurately predict component end of life. In addition, an understanding of the ability of these components and mechanisms to operate under-sodium with the chosen materials will be accomplished. Again, this Gripper Test Assembly is the follow-on test article to the Gear Test Assembly which was testing the ability of gears and bearings operating in a sodium environment. Once fabricated and qualified, it will be tested in the Mechanism Engineering Test Loop (METL) facility located in Building 308 at Argonne National Laboratory.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
In-Space Assembly Capability Assessment for Potential Human Exploration and Science Applications
Human missions to Mars present several major challenges that must be overcome, including delivering multiple large mass and volume elements, keeping the crew safe and productive, meeting cost constraints, and ensuring a sustainable campaign. Traditional methods for executing human Mars missions minimize or eliminate in-space assembly, which provides a narrow range of options for addressing these challenges and limits the types of missions that can be performed. This paper discusses recent work to evaluate how the inclusion of in-space assembly in space mission architectural concepts could provide novel solutions to address these challenges by increasing operational flexibility, robustness, risk reduction, crew health and safety, and sustainability. A hierarchical framework is presented to characterize assembly strategies, assembly tasks, and the required capabilities to assemble mission systems in space. The framework is used to identify general mission system design considerations and assembly system characteristics by assembly strategy. These general approaches are then applied to identify potential in-space assembly applications to address each challenge. Through this process, several focus areas were identified where applications of in-space assembly could affect multiple challenges. Each focus area was developed to identify functions, potential assembly solutions and operations, key architectural trades, and potential considerations and implications of implementation. This paper helps to identify key areas to investigate were potentially significant gains in addressing the challenges with human missions to Mars may be realized, and creates a foundation on which to further develop and analyze in-space assembly concepts and assembly-based architectures.
Jefferies, Sharon A.↗
Revealing and Engineering Assembly Pathways of 3D DNA Origami Crystals
Recent developments in nanomaterial self-assembly demonstrate the capability to create tailored nanostructures by engineering both the binding coordination and specificity of interactions between material subunits. DNA origami frames allow for the design and fabrication of a broad variety of ordered 3D nanoscale architectures through self-assembly, facilitated by frame-to-frame bonds with designable strength and specificity. While the bond design is critical to lattice formation, the assembly process itself is often dependent on a thermal pathway. Highly ordered nanoscale frameworks, assembled from DNA frames, are predominantly crystallized through thermal annealing pathways that typically follow a “slow” cooling approach, with experiments on the time scale of days yielding DNA origami crystals in the range of 1−10 μm. This extended assembly time scale hinders the study of crystal formation pathways, necessitating a deeper understanding of factors governing successful annealing. Lack of insight into time scale also presents a practical limitation for material fabrication. Here, we investigate key factors affecting lattice assembly pathways and demonstrate that precise engineering of assembly conditions greatly reduces assembly times by up to nearly 2 orders of magnitude. We evaluate the nucleation and growth of crystals via optical and electron microscopy, and small-angle X-ray scattering techniques, mapping the time−temperature-transformation of superlattices from the melt through single-crystal optical tracking. The results show that origami frame assembly can be described by classical nucleation and growth theory, which can, in turn, be used to prescribe the growth of the crystals. Lastly, these findings are applied to demonstrate thermal pathway-dependent assembly, forming distinct assemblies based on different thermal annealing profiles.
36 MATERIALS SCIENCE↗
Hierarchical Assembly of Plasmonic Nanoparticle Heterodimer Arrays with Tunable Sub-5 nm Nanogaps
Nanoparticle assemblies have generated intense interest because of their novel optical, electronic, and magnetic properties that open up numerous opportunities in fundamental and applied nanophotonics, -electronics, and -magnetics. However, despite the great scientific and technological potential of these structures, it remains an outstanding challenge to reliably fabricate such assemblies with both nanometer-level structural control and precise spatial arrangements on a macroscopic scale. It is the combination of these two features that is key to realizing nanoparticle assemblies potential, particular for device applications. To address this challenge, we propose a hierarchical assembly approach consisting of both template-particle and particle-particle interactions, whereby the former ensures precise addressability of assemblies on a surface and the latter provides nanometer-level structural control. Template-particle interactions are harnessed via chemical-pattern-directed assembly, and the particle-particle interactions are controlled using DNA-directed self-assembly. To demonstrate the potential of this hierarchical assembly approach, we demonstrate the fabrication of a particularly fascinating assembly: the nanoparticle heterodimer, which possesses a surprisingly rich set of plasmonic properties and is a promising candidate to enable a variety of imaging and sensing applications. Each heterodimer is placed on the surface at predetermined locations, and the precise control of the nanogaps is confirmed by far-field scattering measurements of individual dimers. We further demonstrate that the gap size can be effectively tuned by varying the DNA length. By correlating measured spectra with finite-difference time-domain (FDTD) simulations, we determine the gap sizes to be 4.2 and 5.0 nm-with subnm deviation-for the two DNA lengths investigated. This is one of the best gap uniformities ever demonstrated for surface-bound nanoparticle assemblies. The estimated surface-enhanced Raman scattering (SERS) enhancement factor of these heterodimers is on the order of 10 5 -10 6 with high reproducibility and predictable polarization-dependence. This hierarchical fabrication technique-employing both template-particle and particle-particle interactions-constitutes a novel platform for the realization of functional nanoparticle assemblies on surfaces and thereby creates new opportunities to implement these structures in a variety of applications.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
X-ray and gamma-ray tomographic imaging of fuel relocation inside sodium fast reactor test assemblies during severe accidents
The present work reports on x-ray and gamma-ray high-spatial resolution computerized tomography measurements of the Pin Bundle Metallic Fuel Relocation (PBR) assemblies tested in the Metallic Uranium Safety Experiment (MUSE) facility at Argonne National Lab (ANL). The aim of the study was to characterize fuel relocation structures that develop during severe core accidents pertaining to SFR assemblies; these include but are not limited to advanced core disruption recreated in the PBR-1 assembly, and cladding breach recreated in the PBR-2 assembly. We report the x-ray tomography measurements were able to resolve small quantities of relocation fuel; with increased presence of relocation fuel, the x-ray 1measurements spatially mapped the material but could not resolve the inner regions of these. The gamma-tomography measurements showed improved results, resolving the relocation structures in great detail. The upper plenum of the PBR-1 assembly where the molten uranium was initially inserted presented high structural damage, reflected by the partial and complete disintegration of the central rods. Relocation fuel filled the subchannels, adhering to surviving cladding walls and the assembly casing. In the lower portion of the measured section, the tomogram degrades due to photon starvation effects hinting at the increased amount of relocation fuel potentially plugging the assembly; flow blockage in this section was difficult to determine due to the tomogram’s degradation from photon starvation. Small fragments were observed further down the assembly, dislodged from the initial insertion of the molten material. This section was used as an unperturbed assembly reference, with a calculated blockage of less than 1% from the present fragments. The PBR-2 assembly was characterized by columnar relocation structures propagating through the subchannels. Three of the relocation structures were captured in the measured section, with evidence of cross migration on to adjacent subchannels. The measured section in this assembly captures the leading edge of two structures. The calculated flow blockage was 16% in the planes where the three relocation structures are present, but this quickly decreases to approximately 5% past the leading edge of two of the structures.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
A Lumped Stochastic Model of Coupled Neutronic Assemblies
The objective of the present work is to apply the Harris ansatz to coupled assemblies in a lumped setting, i.e., ignoring the neutron phase dependence, which hitherto has not been considered. A Master equation for the single-time joint distribution of neutron number in each assembly, accounting for transfer of neutrons from one assembly to another via leakage transition probabilities and intercept or view factors is derived from which equations for the mean and variance in each assembly are developed. Because of the neutronic coupling, it is necessary to additionally compute the correlation function between pairs of assemblies which gives an expanded set of moment equations to solve. The reactivity of each assembly is allowed to vary with time, although a formal mechanism that is responsible for reactivity coupling between assemblies is not considered or proposed. Following Harris, it is then hypothesized that the number distribution in each assembly is a gamma distribution with assembly-specific mean and variance computed exactly from the moment equations. Illustrative numerical results are presented for the moments of a system of four coupled assemblies under various reactivity and neutronic coupling scenarios. The gamma distribution is then used to compute the probability that the neutron population exceeds a threshold value in any assembly. The report concludes with a discussion of recommended further work on this problem.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Full Length Assembly Testing in PELICAN (Final Report)
In support of the development of the U.S. Department of Energy (DOE) Versatile Test Reactor (VTR), a thermal hydraulics test facility was constructed to generate experimental measurement of the pressure drop across a single full-scale assembly containing prototypic axial reflectors, fuel, and plena components. Constructed and operated at Argonne National Laboratory, the Pressure drop Experimental Loop for Investigations of Core Assemblies in Nuclear reactors (PELICAN) facility was designed to achieve hydraulic conditions identical to those anticipated for a full-scale fuel assembly located in the VTR core in the region with the highest flow rate. Using water as surrogate for liquid sodium, the flow loop was operated at elevated temperatures and pressures to match the thermophysical properties of liquid sodium and ensure matching Reynolds and Euler numbers. The measurement objectives for data generated from this test facility was driven primarily by the validation needs for code calculations and simulations of the reference VTR core. These objectives focused on the need to validate pressure drop results across the various segments of the fuel assembly as they relate directly to the pumping power and safety of the reactor. Presented in this report are experimental results and analytical comparisons based on testing of a full-length assembly in PELICAN. Housed within a hexagonal test section extending 3.4 m in length, the tested assembly features a prototypic lower reflector, grid plates, wire-wrapped rod bundle, upper reflector, and exit region. The rod bundle extends over 1.5 m in length and contains 217 individual wire-wrapped rods with dimensions that best reflect the reference VTR design. The as-tested bundle assembly was fabricated using 316 stainless steel 0.25-inch (6.35-mm) diameter rods wrapped with 0.04-inch (1.016-mm) diameter wire at a helical pitch of 10.51 inch (26.6 cm). Details of the method for in-house wire-wrapping, assembly, and installation are provided later in this report. Experimental measurements of pressure drop at 19 positions along the test assembly were recorded for a range of flow conditions, with special attention paid to key locations within the assembly, including component inlet and outlet, transition, and wire-wrapped rod bundle regions. Testing conditions were based on 110°C water with flow rates ranging from 50 to 450 GPM (3 to 27 kg/s) at the inlet of the test assembly generating Reynolds numbers and velocities up to ~8.0×10 4 and ~7.8 m/s, respectively, within the rod bundle region. Non-dimensional values for the friction factor were then calculated based on these experimental measurements and compared against those predicted by various analytical correlations available from open literature. Predictions by the upgraded Cheng and Todreas, Rehme, and Novendstern correlations fell within 4% to those values measured experimentally.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗