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Advanced Data Structures for Improved Cyber Resilience and Awareness in Untrusted Environments: LDRD Report

This report summarizes the work performed under the project "Advanced Data Structures for Improved Cyber Resilience and Awareness in Untrusted Environments." The goal of the project was to design, analyze, and test new data structures for cybersecurity applications. We had two major thrusts: 1) using new/improved write-optimized data structures and/or algorithms to better man- age and analyze high-speed massive-volume cyberstreams, and 2) adding security features to data structures at minimum cost. Write optimization allows data structures to better use secondary memory to store and search a larger amount of useful information. Secondary memory is large compared to main memory, but data movement to and from secondary memory must be carefully managed to run quickly enough to keep up with fast streams. The first thrust included managing cyberstreams in parallel, both multi-threaded and distributed, and improving the benchmarking infrastructure for testing new streaming data structures. We considered both (near) real-time discovery of particular patterns, and improved logging for improved forensics. We considered two kinds of security-feature problem. The first was high-performance history- independent external-memory data structures. These provide certain protections to data if a disk is stolen. We also prove some trade-offs between speed and security in this setting. The second data-security problem is more secure data look-up in secret-shared data bases. This report summarizes the project's major accomplishments, with the background to under- stand these accomplishments. It gathers the abstracts and references for the six refereed publications that have appeared as part of this work. We summarize several accomplishments that will be submitted for publication. We then archive one piece of partial work that is not likely to be published in the near future: validation of history-independent data structure implementations.

97 MATHEMATICS AND COMPUTING↗

Sensing and Sampling of Trace Contaminations by a Dexterous Hexrotor UAV at Nuclear Facilities - 18600

Safe and efficient cleanups are a priority for decontamination and decommissioning of nuclear facilities. The contaminations of byproducts and wastes in such nuclear facilities pose a serious problems while decommissioning, to both the operators and public. Sensing these contaminations and cleaning them is an essential part of the safety procedures. The contaminations might range from low-energy to high-energy byproducts. Sensing these byproducts would require contact based or non-contact based sensing, based on its energy levels. Byproducts such as americium, are low-energy which makes it difficult to sense and sample without contact. Therefore, the workers need to physically swab the surfaces to collect the samples of these contaminations. These tasks pose a great danger for the safety of the human workers which includes the risk to reach greater heights, exposure to the radiation and sampling the entire building. A robotic solution is much more desirable in these cases, where the worker can safely handle the contaminations from a safe area. Use of robotic technologies inside these hazardous environments ensures the safety and enhances the performance. The more suitable robotic solution for reaching great heights and covering large areas of nuclear facilities, are aerial vehicles. Multi-rotor unmanned aerial vehicle (UAV) are chosen for their ability to hover at a position and also fly around in confined spaces. Quadrotors are a common choice of multi-rotor UAVs both research and industry because of its ease to fly and commercial availability. For the applications during the cleanups we need the UAV to not only hover and fly in confined spaces, but also interact with the physical world. Despite of quadrotor's advantages, they are not a best suit as they can't interact with the physical world. The tasks involving physical interactions would require the UAV to apply arbitrary forces and torques in all six degrees of freedom (DOF). As quadrotors are under-actuated and non-holonomic in motion, they cannot exert all the required forces. At Collaborative Robotics Lab, Purdue University, we developed a novel multi-rotor UAV solution, Dexterous Hexrotor, which can exert arbitrary forces and torques in all six DOF, independently and instantaneously. This enables the UAV platform to quickly respond to the external disturbances and precisely hold its position during the mission. The Dexterous Hexrotor serves as a robotic tool for the workers to perform sensing and sampling during the cleanups. Workers can operate Dexterous Hexrotor manually and/or semi-autonomously with human intervention. Manual control requires the worker to fly the Dexterous Hexrotor using a remote control. So the workers should possess knowledge on flying the UAV and to perform physical interaction. A semiautonomous Dexterous Hexrotor requires human input to some extent and requires very less knowledge of flying. The autonomy is designed to operate in flight mode and sampling mode. In flight mode, Dexterous Hexrotor takes off from a 'safe' area, reaches the desired altitude, and fly autonomously towards a sampling point. This sampling point is the target position specified on the 2D reference map. This mode also includes navigation towards the sampling point, avoiding the obstacles in the constrained environment. After reaching a stopping point, Dexterous Hexrotor waits for the human input for a target location to swab and collect samples. The Dexterous Hexrotor is now in sampling mode and waits for the human input. The human operator selects the swabbing location through the live streaming video from onboard camera. Through visual servoing, aided by the map, the UAV will move closer towards the target position. It then transitions to the impact control scheme to perform physical interaction with the wall and collects samples. Once the sample is collected, it autonomously returns back to the takeoff position in 'safe' area for the analysis by mass spectrometry. In this paper, we majorly focus on the physical interaction strategy and the required components which enables the autonomy. Decommissioning of nuclear facilities requires decontamination inside the entire buildings. Decontamination of nuclear facilities involves sensing and sampling the huge buildings, long shafts, etc. Sampling the entire facility is not possible due to the limitation in Dexterous Hexrotor's flight time. But this can be achieved by using a swarm of Dexterous Hexrotors to cover larger areas. The onboard robotic arm can be designed based on the applications such as cleaning, applying sealants, etc. The modularity of the design allows us to switch components as per the requirements of the task. These kind of robotic solutions functioning as tools for the workers, aims to make the work environment safer and playful. (authors)

42 ENGINEERING↗

Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment

Lipids have numerous roles critical to living systems. Many of these vital functions are tightly linked or regulated by proteins. Even though the function of many lipid-related enzymes is known, direct links between most individual lipid species and the enzymes that metabolize them are severely lacking. This missing connection impedes biological progress. A resource that allows users to quickly identify protein-lipid relationships will advance our understanding of lipid homeostasis and metabolic perturbed systems. Databases are readily available for mapping small molecule metabolites (i.e., polar metabolites) and specific oxidized fatty acid lipids (e.g., arachidonic acid derivatives) to proteins/enzymes known to be directly involved in metabolism of these molecules (e.g. SMPDB, Reactome, HMDB, BioCyc). This enables the integration of metabolite and protein (as well as transcript) data when performing functional enrichment and metabolic modeling allowing researchers to rapidly examine metabolic pathways from multiple omics sources. Currently, linking lipidomics data with proteomics data is conducted using a time-intensive, user defined, manual process. Here we propose creating a tool that will link lipidomics and proteomics data and also conduct functional enrichment analysis and visualization allowing for full statistical integration. Using text-mining approaches, we will extract lipid references from uniprot and create a database linking lipid species to enzymes directly related to their metabolism. We will also extract directional annotation, which will allow even greater specificity when linking data types and will help eliminate false positives from functional associations.

59 BASIC BIOLOGICAL SCIENCES↗

Lightweight Metal Stamping Optimization Enabled by Artificial Intelligence

Successfully manufacturing an automotive body structure made via the sheet metal stamping process depends upon simultaneous consideration of component design, tooling design, stamping process control, and material properties. In many cases, introducing lightweight sheet materials (e.g., aluminum alloys, magnesium alloys, advanced high strength steels) holds the potential to significantly reduce vehicle weight, but challenges the stamping process by introducing materials with inherently less ductility. Successful and repeatable applications require co-developing the stamping process controls with the varying material properties, including formability. During the stamping process, as soon as the forming limit of the sheet is exceeded, the material shows localized necking which quickly leads to splits. Controlling process variability to avoid these material splits will enable deployment of less formable, lighter, and stronger materials for stamped automotive components. A typical optimization procedure for manufacturing requires an iterative process involving parameter setting, execution of computational simulations, and modifying the parameters. The entire process demands substantial computational time, making it impractical for real-time feedback towards rapid corrective actions required for in-line control for running production processes. To overcome this challenge, artificial intelligence (AI) can be leveraged to determine optimal manufacturing parameters within a single manufacturing cycle time. This research proposes an in-line optimization framework incorporating a trained AI model to predict kidney-shaped die forming. Preliminary results indicate that the AI framework can accurately predict draw-in values based on a given parameter set, a process referred to as forward prediction. Furthermore, the AI framework can also predict the optimal parameter set that leads to the desired draw-in values, referred to as inverse optimization (or backward prediction). This research has been performed in collaborations with USCAR (US Council for Automotive Research) and AutoForm. The members of USCAR are Ford, GM, and Stellantis.

36 MATERIALS SCIENCE↗

Bayesian Inference of the Symmetry Energy of Superdense Neutron-rich Matter from Future Radius Measurements of Massive Neutron Stars

In this work, using as references the posterior probability distribution functions of the equation of state (EOS) parameters inferred from the radii of canonical neutron stars (NSs) reported by the LIGO/VIRGO and NICER Collaborations based on their observations of GW170817 and PSR J0030+0451, we investigate how future radius measurements of more massive NSs will improve our current knowledge about the EOS of superdense neutron-rich nuclear matter, especially its symmetry energy term. Within the Bayesian statistical approach using an explicitly isospin-dependent parametric EOS for the core of NSs, we infer the EOS parameters of superdense neutron-rich nuclear matter from three sets of imagined mass–radius correlation data representing typical predictions by various nuclear many-body theories, that is, the radius stays the same, decreases, or increases with increasing NS mass within ±15% between 1.4 and 2.0 M$_\odot$. The corresponding NS average density increases quickly or slowly or slightly decreases as the NS mass increases from 1.4 to 2.0 M$_\odot$. While the EOSs of symmetric nuclear matter (SNM) inferred from the three data sets are approximately the same, the corresponding symmetry energies above about twice the saturation density of nuclear matter are very different, indicating that the radii of massive NSs carry important information about the high-density behavior of nuclear symmetry energy with little influence from the remaining uncertainties of the SNM EOS at suprasaturation densities.

79 ASTRONOMY AND ASTROPHYSICS↗

AGR-5/6/7 Fuel Fabrication Report

The U.S. Department of Energy Office of Nuclear Energy (DOE NE) and the Idaho National Laboratory (INL) Advanced Reactor Technologies (ART) Advanced Gas Reactor (AGR) Fuel Development and Qualification program (referred to as AGR Fuel program hereafter) are pursuing qualification of tristructural isotropic (TRISO) coated particle fuel for use in high temperature gas cooled reactors (HTGRs). The AGR Fuel program was established to provide a fuel qualification data set in support of the licensing and operation of an HTGR. BWX Technologies Nuclear Operations Group (BWXT-NOG) was subcontracted to fabricate the fuel for the AGR program. Several investments and innovations were realized in preparation to fabricate fuel for the AGR-5/6/7 irradiation experiments that brought fuel fabrication fully out of the laboratory and into engineering-scale operations. These included: • Increased the kernel fabrication line capacity and uniformity • Upgraded ancillary support equipment and processes for the tristructural isotropic (TRISO) coating furnace • Demonstrated efficient production of the matrix precursor powder by dry jet milling of co mingled components • Demonstrated an engineering-scale method for quick and efficient overcoating TRISO particles with the matrix precursor • Demonstrated an automated, multi cavity compacting system with a volumetric feed system • Demonstrated a combined-cycle thermal treatment furnace These changes increased production rates of some of these processes by an order of magnitude or more while eliminating the use of flammable solvents, multiple grinding and sorting operations, and the weighing out of individual die charges. Three fuel kernel lots were fabricated for production of the fuel for AGR-5/6/7. The initial lot (J52R-16-39316) was certified to fuel specifications but was not used because the kernels had a high fraction of internal fissures that caused an unacceptable fraction of the kernels to fragment when charged to the coating furnace where the TRISO coating would be deposited. Fragmented kernels increased the dispersed uranium in the particles and produced a worrisome fraction of dimpled particles with an elevated probability of in-pile failure. After some efforts to identify the cause of the fissure formation, two additional lots were produced with much lower fissure fractions, J52R-16-69317 and 69318. The latter kernel lot was a backup to the first and was not needed. Multiple kernel batches were composited to form each of the lots so as to simulate a commercial-scale operation where kernel batches would also be composited. Multiple TRISO coating runs were performed and the product characterized so that several could be composited into a TRISO lot. TRISO lot J52R-16-98005 conformed to all fuel specifications except the mean outer pyrocarbon (OPyC) layer thickness was thinner than specified. Furthermore, it was determined that the TRISO lot had a dispersed uranium fraction (DUF) that might result in the compacts not meeting the DUF specification. A review of the role of the OPyC layer and consequences of the DUF by the Technical Coordination Team and INL concluded that the fuel was acceptable for use in the AGR-5/6/7 irradiation experiment. The TRISO particles were overcoated with the matrix precursor that had been produced in a jet-milling operation. The overcoating was performed in equipment originally designed to coat pharmaceuticals. The overcoating process performed well; producing highly spherical and uniform overcoats requiring little upgrading and no recycle or rework. TRISO particles were overcoated with the matrix precursor to achieve nominal volumetric packing fractions (PFs) of TRISO particles of 25% and 40% for the irradiation experiments. The 40% PF compacts occupy the first and fifth test capsule in the test train while the inner three capsules are loaded with 25% PF compacts. The resinated graphite matrix precursor powder was a derivative of the German A3-27 matrix formulation, which differs from previous AGR irradiation campaigns that used an A3-3 formulation. Jet milling of the matrix powder precursor produced a finer mean graphite particle size than the milling operations used for the A3-3 matrix powder precursor. Changes made in the matrix formula and equipment yielded compacts with significantly higher matrix density than was attained in previous AGR irradiation campaigns. The changes in the matrix formulation and the means of milling the powders also complicated resolution of the three fuel compact defect fractions, DUF, exposed kernel fraction (EKF), and the silicon carbide defect fraction (SDF). Characterization data from BWXT-NOG had some anomalous results, so samples of the fuel compacts and overcoated TRISO particles were also analyzed by Oak Ridge National Laboratory (ORNL) to ensure that the defect fractions were accurately characterized.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Lead leaching and electrowinning in acetic acid for solar module recycling

It is imperative to recover lead (Pb) contained in end-of-life solar modules. In this paper, a two-step leaching and electrowinning process using acetic acid is investigated for Pb recovery. Acetic acid with hydrogen peroxide can dissolve Pb quickly and, under some conditions, in a matter of minutes. Pb electrowinning has been successfully demonstrated from aqueous solutions of 0.009 M lead(II) acetate with 0–10% v/v acetic acid. Pb-containing deposits are found on both the copper cathode and graphite anode. X-ray diffraction, energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectroscopy confirm the presence of metallic Pb and Pb(II) oxide (PbO) co-deposits on the cathode. Further, there is also the formation of lead subacetate on the cathode under certain conditions. On the anode, the deposit consists of lead(IV) oxide and superoxide (PbO 2 and Pb 1–x O 2 ). A Pb recovery rate of 99% is achieved in 0.009 M lead(II) acetate solutions with 10% v/v acetic acid by applying a reduction potential of either –0.8 V or –1.0 V versus the silver/silver chloride reference electrode for 24h. Pb leaching with acetic acid is also demonstrated from milled silicon solar modules.

14 SOLAR ENERGY↗

Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics

Computational methods for creating in silico libraries of molecular descriptors (e.g., collision cross sections) are becoming increasingly prevalent due to the limited number of authentic reference materials available for traditional library building. These so-called “reference-free metabolomics” methods require sampling sets of molecular conformers in order to produce high accuracy property predictions. Due to the computational cost of the subsequent calculations for each conformer, there is a need to sample the most relevant subset and avoid repeating calculations on conformers that are nearly identical. The goal of this study is to introduce a heuristic method of finding the most dissimilar conformers from a larger population in order to help speed up reference-free calculation methods and maintain a high property prediction accuracy. Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population size grows large. Because there exists a pairwise relationship between each item and all other items in the population, finding the set of the n most dissimilar items is different than simply sorting an array of numbers. For instance, if you have a set of the most dissimilar n = 4 items, one or more of the items from n = 4 might not be in the set n = 5. An exact solution would have to search all possible combinations of size n in the population exhaustively. We present an open-source software called similarity downselection (SDS), written in Python and freely available on GitHub. SDS implements a heuristic algorithm for quickly finding the approximate set(s) of the n most dissimilar items. We benchmark SDS against a Monte Carlo method, which attempts to find the exact solution through repeated random sampling. We show that for SDS to find the set of n most dissimilar conformers, our method is not only orders of magnitude faster, but it is also more accurate than running Monte Carlo for 1,000,000 iterations, each searching for set sizes n = 3–7 out of a population of 50,000. We also benchmark SDS against the exact solution for example small populations, showing that SDS produces a solution close to the exact solution in these instances. Using theoretical approaches, we also demonstrate the constraints of the greedy algorithm and its efficacy as a ratio to the exact solution.

97 MATHEMATICS AND COMPUTING↗

Interaction of Anisole on Alumina-Supported Ni and Mo Oxide Hydrodeoxygenation Catalysts

The conversion of biomass to transportation fuels and value-added chemicals is a promising method to reduce reliance on fossil fuels. Mo-based catalysts have been shown to be highly active in the hydrodeoxygenation of biomass-derived phenolic compounds. The catalyst active phase, surface species, and the effect of adding additional metals is not comprehensively understood. Here we compare the temperature-dependent adsorption behavior of the model compound anisole 2 on an alumina-supported mixed nickel molybdenum oxide catalyst with two reference catalysts of molybdenum oxide and nickel oxide. Raman spectroscopy showed that the catalysts contain significant amounts of molybdates and molybdoaluminates, in addition to NiMoO 4 in the nickel molybdenum catalyst and MoO 3 in the molybdenum-only catalyst. Using transmission infrared spectroscopy under a controlled environment, we find that anisole chemisorbed largely through the oxygen in the methoxy group to form surface-bound phenoxy and methoxy species on all the catalysts. Ambient pressure X-ray photoelectrons spectroscopy measurements of the catalysts in anisole vapor showed reduced Mo atoms are the binding sites. The surface interaction and removal temperature of these species varied with the metal composition. The MoO x component dominated the adsorption behavior in both MoO x and NiMoO x catalysts. The formation of new aromatics, including methylated rings, depended on Ni composition. Upon adding hydrogen to induce the hydrodeoxygenation of anisole, undesirable polynuclear aromatic species were quickly formed on the Mo-based catalysts. In conclusion, these results suggest that the molybdenum oxide controls the adsorption and reactivity of the surface species, with a cooperative effect by Ni.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sensor Placement Optimization using Chama

Continuous or regularly scheduled monitoring has the potential to quickly identify changes in the environment. However, even with low - cost sensors, only a limited number of sensors can be deployed. The physical placement of these sensors, along with the sensor technology and operating conditions, can have a large impact on the performance of a monitoring strategy. Chama is an open source Python package which includes mixed - integer, stochastic programming formulations to determine sensor locations and technology that maximize monitoring effectiveness. The methods in Chama are general and can be applied to a wide range of applications. Chama is currently being used to design sensor networks to monitor airborne pollutants and to monitor water quality in water distribution systems. The following documentation includes installation instructions and examples, description of software features, and software license. The software is intended to be used by regulatory agencies, industry, and the research community. It is assumed that the reader is familiar with the Python Programming Language. References are included for addit ional background on software components. Online documentation, hosted at http://chama.readthedocs.io/, will be updated as new features are added. The online version includes API documentation .

47 OTHER INSTRUMENTATION↗

Data-enabled structure–property mappings for lanthanide-activated inorganic scintillators

The use of machine learning (ML) models toward development of validated structure–property relationships for two fundamental properties of activated inorganic scintillators for high energy radiation detection, namely the light yield (LY) and the decay time constant, is explored. The ML models are built on easily accessible proxies of materials—interchangeably referred to as features, descriptors or fingerprints—that are carefully selected on the basis of a physical understanding of the scintillation mechanism. Our study indicates that the developed physics-based ML models employing kernel ridge regression (KRR) and AdaBoost algorithm applied on top of a decision tree-based regression are able to “learn” the underlying design rules in a multi-dimensional feature space and thereby enable reasonably accurate predictions of the two target properties on unseen compounds (i.e., on a held-out test set). For instance, within a set of twenty-five cerium- or europium-doped scintillator materials, our analysis reveals a strong correlation between the average ionic part of the dielectric constant and the LY, irrespective of the specific chemistry of the compounds, indicating that the average ionic part of the dielectric constant is a particularly relevant descriptor toward prediction of the LY. Our results also demonstrate that, despite the use of small training datasets, the developed models are able to quickly distinguish high performing chemistries from those with relatively poor performance and therefore can play a crucial role in screening of new compounds with an attractive combination of targeted properties. Finally, the present study provides necessary motivation for future efforts involving ML models with relatively large training datasets, vast feature space explorations, and experimental design in search of promising novel scintillator chemistries.

36 MATERIALS SCIENCE↗

Assessing Electronic Structure Methods for Long-Range Three-Body Dispersion Interactions: Analysis and Calculations on Well-Separated Metal Atom Trimers

Three-body dispersion interactions are much weaker than their two-body counterpart. However, their importance grows quickly as the number of interacting monomers rises. To explore the numerical performance of correlation methods for long-range three-body dispersion, we performed calculations on eight very simple dispersion-dominated model metal trimers: Na 3 , Mg 3 , Zn 3 , Cd 3 , Hg 3 , Cu 3 , Ag 3 , and Au 3 . One encouraging aspect is that relatively small basis sets of augmented triple-ζ size appear to be adequate for three-body dispersion in the long-range. Coupled cluster calculations were performed at high levels to assess MP3, CCSD, CCSD(T), empirical density functional theory dispersion (D3), and the many-body dispersion (MBD) approach. We found that the accuracy of CCSD(T) was generally significantly lower than for two-body interactions, with errors sometimes reaching 20% in the investigated systems, while CCSD and particularly MP3 were generally more erratic. MBD is found to perform better than D3 at large distances, whereas the opposite is true at shorter distances. When computing reference numbers for three-body dispersion, care should be taken to appropriately represent the effect of the connected triple excitations, which are significant in most cases and incompletely approximated by CCSD(T).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Durability of Disposable N95 Mask Material When Exposed to Improvised Ozone Gas Disinfection

The principle finding of this report is that both commercial and a novel material used for N95 mask filters can endure many cycles of disinfection by ozone gas (20 ppm for 30 minutes) without detectable degradation or loss of filtration efficiency. N95 masks and surgical masks (hereafter referred to as masks) typically use a filtration material fabricated from meltblown polypropylene. To achieve maximum filtration efficiency while maintaining a reasonable pressure drop, these nonwoven fabrics are also electrostatically charged (corona discharge is the most common method used), to maximize attraction and capture of aerosols and solid particulates. Under normal circumstances, the reuse of masks is generally discouraged, but in times of crisis has become a necessity, making disinfection after each use a necessity. To be acceptable, any disinfection procedure must cause minimal degradation to the performance of the filter material. Possible performance degradation mechanisms include mechanical damage, loss of electrostatic charge, or both. One of the most practical and direct ways to measure combined mechanical and electrostatic integrity, and the subsequent ability to reuse mask filter material, is by the direct measurement of filtration efficiency. In this paper, we report that small numbers of disinfection cycles at reasonable virucidal doses of ozone do not significantly degrade the filtration efficiency of meltblown polypropylene filter material. By comparison, laundering quickly results in a significant loss of filtration efficiency and requires subsequent recharging to restore the electrostatic charge and filtration efficiency. A common assumption among biomedical scientists that ozone is far too destructive for this application. However, these direct measurements show that mask materials, specifically the filtration material, can withstand dozens of ozone disinfection cycles without any measurable degradation of filtration efficiency, nor any visible discoloration or loss of fiber integrity. The data are clear: when subjected to a virucidal dose of ozone for a much longer duration than is required for viral inactivation, there was no degradation of N95 filtration efficiency. The specific dosages of ozone needed for ~99% viral inactivation are thought to be at least 10 ppm for up to 30 minutes based upon an extensive literature review, but to standardize our testing, we consider a dose of 20 ppm for 30 minutes to be a reasonable and conservatively high ozone disinfection cycle. Finally, the material tested in this study withstood dosages of up to 200 ppm for 90 minutes, or alternatively 20 ppm for up to 36 hours, without detectable degradation, and further testing suggests that up to 30 or more disinfection cycles (at 20 ppm for 30 minutes) would result in less than a 5% loss of filtration efficiency. This report does not address the effect of ozone cycling on other mask components, such as elastics.

60 APPLIED LIFE SCIENCES↗

jialiu232/MetaFunPrimer_paper_info

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably.

Liu, Jia↗

Designing a Framework for Solving Multiobjective Simulation Optimization Problems

Multiobjective simulation optimization (MOSO) problems are optimization problems with multiple conflicting objectives, where evaluation of at least one of the objectives depends on a black-box numerical code or real-world experiment, which we refer to as a simulation. Whereas an extensive body of research is dedicated to developing new algorithms and methods for solving these and related problems, it is challenging and time-consuming to integrate these techniques into real-world production-ready solvers. This is partly because of the diversity and complexity of modern state-of-the-art MOSO algorithms and methods and partly because of the complexity and specificity of many real-world problems and their corresponding computing environments. The complexity of this problem is only compounded when introducing potentially complex and/or domain-specific surrogate-modeling techniques, problem formulations, design spaces, and data acquisition functions. Here, this paper carefully surveys the current state of the art in MOSO algorithms, techniques, and solvers, as well as problem types and computational environments where MOSO is commonly applied. We then present several key challenges in the design of a parallel multiobjective simulation optimization framework (ParMOO) and how they have been addressed. Finally, we provide two case studies demonstrating how customized ParMOO solvers can be quickly built and deployed to solve real-world MOSO problems.

engineering design optimization↗

MESOSCALE THERMAL TRANSPORT MEASUREMENTS OF MULTI-PHASE AND POROUS NUCLEAR FUELS USING A SQUARE-WAVE PULSE THERMOREFLECTANCE TECHNIQUE

The safe and efficient operation of nuclear reactors require accurate knowledge of peak temperatures in the fuel assemblies. The temperature profiles are governed by the thermal transport properties of the fuel, namely the thermal conductivities (k) and thermal diffusivities (D). These values can be very difficult to measure as they are known to vary considerably from the measured bulk values of the fresh fuel, and quickly degrade with increasing burnup [1 -3] . Laser-based techniques have been effectively used for non-destructive and non-contact thermal transport measurements of a wide variety of materials, including nuclear materials [4-6] that would otherwise prove too hazardous or difficult to measure otherwise. In this study, a new thermoreflectance technique known as square-pulse transient thermoreflectance (SPTR) is described and used to determine the mesoscale thermal diffusivity of both uranium sesquisilicide (U3Si2) and uranium nitride (UN) phases in a composite fuel with micron level spatial resolution [7]. This technique employs a rapid train of square-wave pulses from an excitation laser to create a periodic heat flux on a gold coated sample surface. Surface adsorption results in transient film temperatures and hence rapid fluctuations in thermoreflectance that can be measured via a detection laser coupled with a digital oscilloscope. The lasers are coaxially focused on the sample surface, allowing for a sample measurement area of a single convolved laser spot size (~2 µm). A sensitivity analysis was conducted to identify key measurement parameters of this technique using reference materials with a range of thermal conductivities comparable to those of both ceramic, composite, and metal nuclear fuel types (1.4 – 27.2 W/m-K). The reference materials were measured using the new technique as well as a spatial-domain thermoreflectance technique (SDTR) previously reported for a comparison [8]. Additionally, measurements of several U3Si2 and UN phase regions of a polished UN/U3Si2 (70/30 vol.%) sample were taken, and the resulting calculated D values are reported, with both techniques showing excellent agreement between samples. This technique was used to scan a multiphase region at 5 micron increments to generate a local diffusivity map, demonstrating the utility of the techniques for measuring thermal transport properties in specimens with precipitates and secondary phases. Furthermore, the technique is currently being applied to measure thermal properties of Fast Flux Test Reactor (FFTR) irradiated metal fuel specimens whose porous microstructure make it very difficult to measure using other techniques. Comparison of the local scale measurements are compared with the pre-irradiated fuel samples to show the degradation of thermal transport in fuels due to pores from fission gas bubbles and other irradiation induced defects.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Complex Dependence of Calcite Crack Kinetics on Salinity: The Role of DLVO and Hydration Forces

Abstract Subcritical crack growth (SCG) plays an important role in many geological processes such as delayed earth rupture and rock weathering. The complex dependency of SCG on the in‐crack fluid chemistry, however, is still poorly understood. In this study, we utilize the newly developed surface force‐based fracture theory (SFFT) to elucidate the relative contributions of surface forces and solute transport to the crack growth kinetics of calcite in NaCl solutions. Expanding on Barenblatt's cohesive crack model, SFFT introduces an effective stress intensity at the crack tip that encompasses all the relevant intermolecular forces across the crack in addition to the external far‐field stresses. The nonlinear system of equations portraying the crack opening profile, the solute distribution in a propagating crack, and the crack growth velocity are numerically solved via an implicit scheme. After carefully calibrating the model for calcite‐water systems, the SFFT is used to predict the SCG response of calcite at different NaCl concentrations, based on various hypotheses. These predictions are then compared to existing SCG data from the literature. We demonstrate that the experimentally observed variation of SCG rate with NaCl concentration cannot be explained solely by DLVO forces (electrostatic and Van der Waals interactions). This can be remediated by introducing an exponentially decaying hydration force with a nonlinear, nonmonotonic dependence on NaCl concentration. Furthermore, we demonstrate that accounting for both diffusive and advective transport of ions is important in explaining the absence of a stage‐II SCG response for calcite in electrolyte solutions. Plain Language Summary Subcritical crack growth (SCG) refers to the slow propagation of cracks in materials under a stress below the threshold for catastrophic failure. SCG is a key process in many geological events, for example, delayed earth ruptures and rock weathering. New initiatives such as underground CO 2 and H 2 storage in carbonate reservoirs further call for better understanding of SCG in carbonate minerals subjected to varying fluid chemistry. This study examines the SCG of calcite, a key mineral found in carbonate rocks, intergranular cement in sandstones, and filling material in mineral veins and faults, determining their deformation and strength. A mathematical model is developed to describe how the crack opens and propagates, how solutes (like salts) distribute within the crack, and how the crack surfaces interact with each other. We used the model to predict calcite SCG in water at different salt concentrations and compared it with experimental data. Our results revealed that the hydration force is the dominating factor in determining the complex, non‐linear dependency of SCG on salinity. We also found that both the movement of ions by diffusion and by bulk water flow are crucial for explaining the SCG rates, especially when the cracks grow quickly. Key Points Surface Force‐Based Fracture Theory predicts the complex subcritical crack growth patterns of calcite crystals immersed in NaCl solutions Results highlight the dominant role of hydration forces in altering the fracture behavior of calcite compared to VdW and electric double‐layer forces Advective solute transport explains the absence of stages‐II and ‐III subcritical crack growth responses in solid‐liquid systems

DLVO↗

Proposal and evaluation of subordinate standard solar irradiance spectra for applications in solar energy systems

Reference solar irradiance spectra are needed to specify key parameters of solar technologies such as photovoltaic cell efficiency, in a comparable way. The IEC 60904-3 and ASTM G173 standards present such spectra for Direct Normal Irradiance (DNI) and Global Tilted Irradiance (GTI) on a 37 degrees tilted sun-facing surface for one set of clear-sky conditions with an air mass of 1.5 and low aerosol content. The IEC/G173 standard spectra are the widely accepted references for these purposes. Hence, the authors support the future replacement of the outdated ISO 9845 spectra with the IEC spectra within the ongoing update of this ISO standard. The use of a single reference spectrum per component of irradiance is important for clarity when comparing and rating solar devices such as PV cells. However, at some locations the average spectra can differ strongly from those defined in the IEC/G173 standards due to widely different atmospheric conditions and collector tilt angles. Therefore, additional subordinate standard spectra for other atmospheric conditions and tilt angles are of interest for a rough comparison of product performance under representative field conditions, in addition to using the main standard spectrum for product certification under standard test conditions. This simplifies the product selection for solar power systems when a fully-detailed performance analysis is not feasible (e.g. small installations). Also, the effort for a detailed yield analyses can be reduced by decreasing the number of initial product options. After appropriate testing, this contribution suggests a number of additional spectra related to eight sets of atmospheric conditions and tilt angles that are currently considered within ASTM and ISO working groups. The additional spectra, called subordinate standard spectra, are motivated by significant spectral mismatches compared to the IEC/G173 spectra (up to 6.5%, for PV at 37 degrees tilt and 10-15% for CPV). These mismatches correspond to potential accuracy improvements for a quick estimation of the average efficiency by applying the appropriate subordinate standard spectrum instead of the IEC/G173 spectra. The applicability of these spectra for PV performance analyses is confirmed at five test sites, for which subordinate spectra could be intuitively selected based on the average atmospheric aerosol optical depth (AOD) and precipitable water vapor at those locations. The development of subordinate standard spectra for DNI and concentrating solar power (CSP) and concentrating PV (CPV) is also considered. However, it is found that many more sets of atmospheric conditions would be required to allow the intuitive selection of DNI spectra for the five test sites, due in particular to the stronger effect of AOD on DNI compared to GTI. In conclusion, the matrix of subordinate GTI spectra described in this paper are recommended to appear as an option in the annex of future standards, in addition to the obligatory use of the main spectrum from the ASTM G173 and IEC 60904 standards.

14 SOLAR ENERGY↗