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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2015

GISAXS study of Au-coated light-induced polymer gratings

Surface Relief Gratings (SRGs) are inscribed in the Au-coated azobenzene containing photosensitive polymer films on a glass substrate. The structures consist of micrometer-period sinusoidal patterns of sub-micron amplitudes, formed by photo-isomerization and molecular reorientation processes in the polymer film during exposure to the light interference pattern that drove the formation of a SRG; the precursor is a stack sequence of Au, polymer, and glass. The SRG structures were exposed in GISAXS geometry to high-intensity X-ray radiation from a liquid Ga source (0.134 nm). Scattered photons were registered by a 2D detector, and their intensity distribution enabled us to characterize the structures. Analysis of the 2D patterns yielded information about the pitch of the gratings as well as the thickness of the films forming the gratings. The GISAXS experiments were carried out at the Research Center Juelich.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

Improved third generation peristaltic crawler for removal of high-level waste plugs in United States department of energy Hanford site pipelines

There are approximately 56 million gallons (212 km{sup 3}) of high level waste (HLW) at the U.S. Department of Energy (DOE) Hanford Site. It is scheduled that by the year 2040, the HLW is to be completely transferred to secure double-shell tanks (DST) from the leaking single-tanks (SST) via transfer pipeline system. Blockages have formed inside the pipes during transport because of the variety in composition and characteristics of the waste. These full and partial plugs delay waste transfers and require manual intervention to repair, therefore are extremely expensive, consuming millions of dollars and further threatening the environment. To successfully continue the transfer of waste through the pipelines, DOE site engineers are in need of a technology that can accurately locate the blockages and unplug the pipelines. In this study, the proposed solution to remediate blockages formed in pipelines is the use of a peristaltic crawler: a pneumatically/hydraulically operated device that propels itself in a worm-like motion through sequential fluctuations of pressure in its air cavities. The crawler is also equipped with a high-pressure water nozzle used to clear blockages inside the pipelines. The crawler is now in its third generation. Previous generations showed limitations in its durability, speed, and maneuverability. Latest improvements include an automation of sequence that prevents kickback, a front-mounted inspection camera for visual feedback, and a thinner wall outer bellow for improved maneuverability. Different experimental tests were conducted to evaluate the improvements of crawler relative to its predecessors using a pipeline test-bed assembly. Anchor force tests, unplugging tests, and fatigue testing for both the bellow and rubber rims have yet to be conducted and thus results are not presented in this research. Experiments tested bellow force and response, cornering maneuverability, and straight line navigational speed. The design concept and experimental test results are reported. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2014

Polariton condensation with saturable molecules dressed by vibrational modes

Here, polaritons, mixed light-matter quasiparticles, undergo a transition to a condensed, macroscopically coherent state at low temperatures or high densities. Recent experiments show that coupling light to organic molecules inside a microcavity allows condensation at room temperature. The molecules act as saturable absorbers with transitions dressed by molecular vibrational modes. Motivated by this, we calculate the phase diagram and spectrum of a modified Tavis-Cummings model, describing vibrationally dressed two-level systems, coupled to a cavity mode. Coupling to vibrational modes can induce re-entrance, i.e. a normal-condensed-normal sequence with decreasing temperature and can drive the transition first-order.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Adaptive Laboratory Evolution for Enhanced Performance of Cupriavidus necator on Formic Acid

The need to decarbonize our economy is becoming ever more pressing. CO2, can be electrochemically reduced to formic acid, a soluble C1 molecule that can be used to store carbon and energy. Cupriavidus necator H16, a soil bacterium, capable of consuming and growing on formic acid as its sole carbon source, is well positioned to upgrade CO2-derived formic acid into value added chemicals such as sustainable aviation fuel. To improve the performance of C. necator on formic acid adaptive laboratory evolution (ALE), a proven tool for improving microbial fitness, has been conducted using continuous pH-stat bioreactors. The system works on the basis that consumption of formic acid raises the pH and triggers the addition of more formic acid to maintain the pH at 6.7, such that formic acid is provided at the same rate as it is consumed. This system has been coupled with level control to achieve continuous fermentation where cells acquiring mutations that improve growth on formic acid become more abundant in the population, from which they can be isolate and characterized. This configuration where the dilution rate is controlled by pH-stat has been found to seek out a dilution rate that matches the exponential growth rate of the organism. During developmental experiments it was discovered that formic acid accumulated to inhibitory levels. It was determined that the nitrogen source, ammonium hydroxide, must be tailored to the carbon consumption to avoid formic acid accumulation. ALE has run in three lineages for 2000+ hours and 300+ generations. Growth of evolved isolates derived from all lineages will be evaluated on formic acid and those with improved growth rates or biomass yield will be subjected to whole genome sequencing to identify potentially causative mutations. These mutations will be evaluated individually and in combination to identify those that improve growth on formic acid.

adaptive laboratory evolution↗

DOE OSTI2021

Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts

The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Deep learning with plasma plume image sequences for anomaly detection and prediction of growth kinetics during pulsed laser deposition

Abstract Materials synthesis platforms that are designed for autonomous experimentation are capable of collecting multimodal diagnostic data that can be utilized for feedback to optimize material properties. Pulsed laser deposition (PLD) is emerging as a viable autonomous synthesis tool, and so the need arises to develop machine learning (ML) techniques that are capable of extracting information from in situ diagnostics. Here, we demonstrate that intensified-CCD image sequences of the plasma plume generated during PLD can be used for anomaly detection and the prediction of thin film growth kinetics. We develop multi-output (2 + 1)D convolutional neural network regression models that extract deep features from plume dynamics that not only correlate with the measured chamber pressure and incident laser energy, but more importantly, predict parameters of an auto-catalytic film growth model derived from in situ laser reflectivity experiments. Our results demonstrate how ML with in situ plume diagnostics data in PLD can be utilized to maintain deposition conditions in an optimal regime. Further, the predictive capabilities of plume dynamics on the kinetics of film growth or other film properties prior to deposition provides a means for rapid pre-screening of growth conditions for the non-expert, which promises to accelerate materials optimization with PLD.

36 MATERIALS SCIENCE↗

DOE OSTI2015

From H i to stars: H I depletion in starbursts and star-forming galaxies in the ALFALFA Hα survey

H i in galaxies traces the fuel for future star formation and reveals the effects of feedback on neutral gas. Using a statistically uniform, H i-selected sample of 565 galaxies from the Arecibo Legacy Fast ALFA (ALFALFA) Hα survey, we explore H i properties as a function of star formation activity. ALFALFA Hα provides R-band and Hα imaging for a volume-limited subset of the 21 cm ALFALFA survey. We identify eight starbursts based on Hα equivalent width and six with enhanced star formation relative to the main sequence. Both starbursts and non-starbursts have similar H i-to-stellar mass ratios (M{sub H I}/M{sub ∗}), which suggests that feedback is not depleting the starbursts’ H i. Consequently, the starbursts do have shorter H i depletion times (t{sub dep}), implying more efficient H i-to-H{sub 2} conversion. While major mergers likely drive this enhanced efficiency in some starbursts, the lowest-mass starbursts may experience periodic bursts, consistent with enhanced scatter in t{sub dep} at low M{sub ∗}. Two starbursts appear to be pre-coalescence mergers; their elevated M{sub H I}/M{sub ∗} suggest that H i-to-H{sub 2} conversion is still ongoing at this stage. By comparing with the GASS sample, we find that t{sub dep} anticorrelates with stellar surface density for disks, while spheroids show no such trend. Among early-type galaxies, t{sub dep} does not correlate with bulge-to-disk ratio; instead, the gas distribution may determine the star formation efficiency. Finally, the weak connection between galaxies’ specific star formation rates and M{sub H I}/M{sub ∗} contrasts with the well-known correlation between M{sub H I}/M{sub ∗} and color. We show that dust extinction can explain the H i–color trend, which may arise from the relationship between M{sub ∗}, M{sub H I}, and metallicity.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Solid-state NMR experiments have been developed to probe crystallization behavior fluoropolymers (Progress Summary)

The FK-800 fluoropolymer elastomer is being developed as a replacement material for the Kel-F 800 binder in the plastic bonded explosive PBX-9502. These polymers are a random co-polymer of poly-vinylidene fluoride (PVDF) and poly-chlorotrifluoroetheylene (PCTFE) in nominal 1:3 ratio. Initial characterizations of the FK-800 replacement show similar characteristics as the legacy Kel-F 800. However, differences in bulk crystallinity and crystallization kinetics have been observed. These differences may be driven by small differences in the distribution of the monomers on the polymer backbone (sequence distribution).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

RNA interference influenced the proliferation and invasion of XWLC-05 lung cancer cells through inhibiting aquaporin 3

Objective: The objective of this study was to construct a recombinant vector expressing siRNA targetedly inhibiting aquaporin 3 (AQP3), and to evaluate the effects of AQP3 inhibition on the proliferation and invasion of XWLC-05 human lung cancer cells. Methods: We obtained human AQP3 sequence from the Genbank and established the recombinant vector expressing siRNA targeting AQP3. After the transfection of the recombinant vectors, the expression of AQP3 was determined by RT-PCR and western blot. The MTS assay, flow cytometry and Transwell assay were conducted to detect the proliferation, cell cycle process, apoptosis and invasion of XWLC-05 cells. Then the activity of metal matrix proteinase (MMP) 2 was determined by gelatin zymography. Tumor formation in vivo experiments were also conducted in nude mice. Results: RNA interference (RNAi) of AQP3 substantially suppressed the XWLC-05 cell proliferation and invasion, blocked the cell cycle progressing and promoted cell apoptosis. In addition, the activity of MMP2 was remarkably attenuated in RNAi group. AQP3 RNAi did not affect the tumor formation rate in nude mice but reduced the tumor growth. Conclusion: The inhibition of AQP3 retarded the growth and invasiveness of XWLC-05 lung cancer cells and decreased the activity of MMP2.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Alternatives to vitamin B 1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages

Here, vitamin B 1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytoplankton as well as taxa from two lineages previously known to have riboswitches (green algae and stramenopiles). The predicted secondary structures bear hallmarks of TPP-sensing riboswitches. Surprisingly, most of the identified riboswitches are affiliated with genes of unknown function, rather than characterized thiamine biosynthesis genes. Using qPCR and growth experiments involving two prasinophyte algae, we show that expression of these genes increases significantly under vitamin B 1 -deplete conditions relative to controls. Pathway analyses show that several algae harboring the uncharacterized genes lack one or more enzymes in the known TPP biosynthesis pathway. We demonstrate that one such alga, the major primary producer Emiliania huxleyi , grows on 4-amino-5-hydroxymethyl-2-methylpyrimidine (a thiamine precursor moiety) alone, although long thought dependent on exogenous sources of thiamine. Thus, overall, we have identified riboswitches in major eukaryotic lineages not known to undergo this form of gene regulation. In these phytoplankton groups, riboswitches are often affiliated with widespread thiamine-responsive genes with as yet uncertain roles in TPP pathways. Further, taxa with ‘incomplete’ TPP biosynthesis pathways do not necessarily require exogenous vitamin B 1 , making vitamin control of phytoplankton blooms more complex than the current paradigm suggests.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Structural Biology of Aromatic Amino Acid Biosynthesis in Plants: The Prephenate Branch Point

Plants are chemists that have spent the last 425 million years evolving unique secondary metabolites to communicate with their surroundings, defend themselves against pathogens, insects, and herbivores, and grow and develop. Many secondary metabolites are biosynthesized from the aromatic amino acids tryptophan, tyrosine, and phenylalanine, and the shikimate and aromatic amino acid biosynthetic pathways link primary and specialized metabolism. Prephenate aminotransferase (PAT) is a key enzyme in aromatic amino acid biosynthesis because its product, arogenate, is the immediate precursor for both tyrosine and phenylalanine. Interestingly, the enzyme has a dual role in metabolism and can also function as a classical aspartate aminotransferase. AtPAT is pyridoxal 5′‐phosphate‐dependent (PLP) enzyme belonging to the AAT‐like aspartate aminotransferase domain and follows a ping‐pong bi‐bi reaction mechanism through Schiff‐base formation to a catalytic K306 in the active site. Each subunit of the AtPAT dimer consists of a large domain and a small domain that belong to the α‐β class of protein fold. Despite the structural similarities to aspartate aminotransferases, the molecular basis of prephenate binding specificity remains elusive. To gain an understanding of the enzyme's chemistry and substrate selectivity, a 2.5 Å x‐ray structure of PAT from the model plant Arabidopsis thaliana (thale cress) was solved in complex with the PLP. To our knowledge, this is the first structure of a bona fide prephenate aminotransferase. Amino acid sequence comparisons of all known functional PATs shows that T84 and K169 are highly conserved; however, some enzymes annotated as PAT display sequence variations at these positions. Biochemical analysis of T84V, K169V, and T84V/K169V PAT reveals that the double mutant gained tyrosine aminotransferase activity and was able to convert 4‐hydroxyphenylpyruvate to tyrosine. T84 is on the opposite side of the active site pocket, while the amine backbone of K169 hydrogen bonds to PLP. We hypothesize that Thr84 and Lys169 are important for substrate recognition in the active site and will use these mutants in future crystallographic experiments. Overall, our structural studies will assist in understanding the role of this bi‐functional enzyme in the context of aromatic amino acid biosynthesis in plants. Support or Funding Information This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE‐1143954. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Results shown in this report are derived from work performed at Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source. Argonne is operated by UChicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE‐AC02‐06CH11357.

Holland, Cynthia K.↗

DOE OSTI2013

Structural Insights into Neutrophilic Migration Revealed by the Crystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1

Neutrophil plays an essential role in host defense against infection, but uncontrolled neutrophilic infiltration can cause inflammation and severe epithelial damage. We recently showed that CXCR2 formed a signaling complex with NHERF1 and PLC-2, and that the formation of this complex was required for intracellular calcium mobilization and neutrophilic transepithelial migration. To uncover the structural basis of the complex formation, we report here the crystal structure of the NHERF1 PDZ1 domain in complex with the C-terminal sequence of CXCR2 at 1.16 Å resolution. The structure reveals that the CXCR2 peptide binds to PDZ1 in an extended conformation with the last four residues making specific side chain interactions. Remarkably, comparison of the structure to previously studied PDZ1 domains has allowed the identification of PDZ1 ligand-specific interactions and the mechanisms that govern PDZ1 target selection diversities. In addition, we show that CXCR2 can bind both NHERF1 PDZ1 and PDZ2 in pulldown experiments, consistent with the observation that the peptide binding pockets of these two PDZ domains are highly structurally conserved. The results of this study therefore provide structural basis for the CXCR2-mediated neutrophilic migration and could have important clinical applications in the prevention and treatment of numerous neutrophil-dependent inflammatory disorders.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Origin and Evolution of Magnetic Field in PMS Stars: Influence of Rotation and Structural Changes

During stellar evolution, especially in the pre-main-sequence phase, stellar structure and rotation evolve significantly, causing major changes in the dynamics and global flows of the star. We wish to assess the consequences of these changes on stellar dynamo, internal magnetic field topology, and activity level. To do so, we have performed a series of 3D HD and MHD simulations with the ASH code. We choose five different models characterized by the radius of their radiative zone following an evolutionary track computed by a 1D stellar evolution code. These models characterized stellar evolution from 1 to 50 Myr. By introducing a seed magnetic field in the fully convective model and spreading its evolved state through all four remaining cases, we observe systematic variations in the dynamical properties and magnetic field amplitude and topology of the models. The five MHD simulations develop a strong dynamo field that can reach an equipartition state between the kinetic and magnetic energies and even superequipartition levels in the faster-rotating cases. We find that the magnetic field amplitude increases as it evolves toward the zero-age main sequence. Moreover, the magnetic field topology becomes more complex, with a decreasing axisymmetric component and a nonaxisymmetric one becoming predominant. The dipolar components decrease as the rotation rate and the size of the radiative core increase. The magnetic fields possess a mixed poloidal-toroidal topology with no obvious dominant component. Moreover, the relaxation of the vestige dynamo magnetic field within the radiative core is found to satisfy MHD stability criteria. Hence, it does not experience a global reconfiguration but slowly relaxes by retaining its mixed stable poloidal-toroidal topology.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

A Hybrid AI/ML and Computational Mechanics Based Approach for Time-Series State and Fatigue Life Estimation of Nuclear Reactor Components

Environmental fatigue modeling is a complex problem due to multiple failure modes and their intermixing. The failure modes are function of various underlying causes in addition to the corrosive effect of reactor coolant environment. Some of the major causes are time-dependence of material associated with cyclic loading, load sequence effect associated with random/variable amplitude loading, effect of strain amplitude and rates, effect of varying temperature (along both temporal and spatial directions) and the effect of mean strain and stress. The nonlinear intermixing of failure modes associated with above mentioned causing parameters makes the environmental fatigue modeling is a challenging task. Because of this challenge, fatigue is traditionally being modeled based on experimental data. However, test based empirical approach often requires hundreds of fatigue tests to model the above-mentioned intermixing failure causes even for a single material system. The problem is further exaggerated for reactor component made from multi-material systems such as made from both carbon and stainless-steel base metals and their similar and dissimilar metal welds. With the difficulty of conducting hundreds of fatigue tests to capture the above-mentioned intermixing failure causes, fatigue modeling approaches often depends on empirical models based on limited available test data such as available through ASME code and NUREG 6909. However, these limited test-data-based models may not be enough to accurately predict the life of reactor components. Accurate prediction of life of reactor component would become a necessity, particularly when the license of the reactors to be extended for long-term-operation (LTO) that is for well beyond its original design life of 40 years. The requirement of extending the license of reactor under LTO requires hundreds of fatigue tests to be conducted to understand the mechanism associated with the above-mentioned interdependent failure causes. However, conducting large number of fatigue tests is not a feasibility due to the cost involved. To address this issues Argonne National Laboratory (ANL) with the sponsorship of DOE Light Water Reactor Sustainability (LWRS) program trying to develop a hybrid predictive modeling approach. This is based on limited experiment-data, Artificial-intelligence (AI) – Machine-Learning (ML) - Deep-Learning (DL) based techniques and Multiphysics-computational-mechanics based modeling tools. The hybrid approach not-only can improve the accuracy of the existing stress analysis and fatigue modeling approach but also can reduce the over-dependency on test-based approach. Towards this goal following are some of the major contributions based on ANL’s FY-20 environmental fatigue modeling activities: 1) A cyclic plasticity material model database for 82/182 dissimilar metal weld, which can be readily shared with US nuclear industry and regulatory agency on request. 2) A well validated analytical modeling methodology to perform cycle-by-cycle stress prediction under both constant amplitude fatigue loading and variable amplitude fatigue loading (with load-sequence effect). 3) An AI/ML/DL based methodology to predict unmeasurable cyclic strain based on other available sensor signals. This type of approach can be used for estimating strain in real reactor components from other sensor readings. 4) An AI/ML based approach to improve the US capability on environmental fatigue testing. This is by improving ANL’s existing environmental fatigue testing capacity to conduct ASME required strain-controlled tests (by controlling strain amplitudes and its rate), while not measuring the strain (due to the difficulty of placing an extensometer in a narrow autoclave in a PWR-water-test system). 5) A simulation and experiment based probabilistic modeling methodology for time-series fatigue state and life estimation of reactor metal such as dissimilar metal weld.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

End-User Perspectives on Using Quantitative Real-Time PCR and Genomic Sequencing in the Field

Quantitative real-time PCR and genomic sequencing have become mainstays for performing molecular detection of biological threat agents in the field. There are notional assessments of the benefits, disadvantages, and challenges that each of these technologies offers according to findings in the literature. However, direct comparison between these two technologies in the context of field-forward operations is lacking. Most market surveys, whether published in print form or provided online, are directed to product manufacturers who can address their respective specifications and operations. One method for comparing these technologies is surveying end-users who are best suited for discussing operational capabilities, as they have hands-on experience with state-of-the-art molecular detection platforms and protocols. These end-users include operators in military defense and first response, as well as various research scientists in the public sector such as government and service laboratories, private sector, and civil society such as academia and nonprofit organizations performing method development and executing these protocols in the field. Our objective was to initiate a survey specific to end-users and their feedback. We developed a questionnaire that asked respondents to (1) determine what technologies they currently use, (2) identify the settings where the technologies are used, whether lab-based or field-forward, and (3) rate the technologies according to a set list of criteria. Of particular interest are assessments of sensitivity, specificity, reproducibility, scalability, portability, and discovery power. This article summarizes the findings from the end-user perspective, highlighting technical and operational challenges.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Controlling effective interactions and spatial dispersion of nanoparticles in multiblock copolymer melts

The microscopic Polymer Reference Interaction Site Model theory is employed to study, for the first time, the effective interactions, spatial organization, and miscibility of dilute spherical nanoparticles in non-microphase separating, chemically heterogeneous, compositionally symmetric AB multiblock copolymer melts of varying monomer sequence or architecture. The dependence of nanoparticle wettability on copolymer sequence and chemistry results in interparticle potentials-of-mean force that are qualitatively different from homopolymers. An important prediction is the ability to improve nanoparticle dispersion via judicious choice of block length and monomer adsorption-strengths which control both local surface segregation and chain connectivity induced packing constraints and frustration. The degree of dispersion also depends strongly on nanoparticle diameter relative to the block contour length. Small particles in copolymers with longer block lengths experience a more homopolymer-like environment which renders them relatively insensitive to copolymer chemical heterogeneity and hinders dispersion. Larger particles (sufficiently larger than the monomer diameter) in copolymers of relatively short block lengths provide better dispersion than either a homopolymer or random copolymer. The theory also predicts a novel widening of the miscibility window for large particles upon increasing the overall molecular weight of copolymers composed of relatively long blocks. The influence of a positive chi-parameter in the pure copolymer melt is briefly studied. Quantitative application to fullerenes in specific copolymers of experimental interest is performed, and miscibility predictions are made.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis

Large scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. To facilitate such efforts, we have developed a suite of codes, collectively referred to as AutoMech, that allow for the automatic prediction of the kinetics for large sets of reactions via ab initio transition-state-theory based master-equation calculations. The primary input is simply the mechanism, a dictionary relating chemically identifiable species descriptors (e.g., SMILES or InChIs) to species labels in the mechanism, and a specification of the electronic structure and transition state theory models to be implemented. Here we illustrate the current utility of AutoMech through a study of the initial stages of pyrolysis for 3 sets of fuels: sequences of alkanes, alcohols, and aldehydes. For simplicity, the analysis focuses on abstractions from the fuel by H, CH 3 , and OH, and the decomposition of the resulting radicals. Altogether, there are a total of 166 input channels in these sets (more than 363 forward reactions when expanded to the full set of elementary reactions). The code successfully produces high quality rate estimates (with apparent uncertainties less than a factor of two in limited comparisons with experiment) for > 95% of these. For the radical decomposition reactions, the analysis includes predictions for the pressure dependence of the kinetics. This wide-ranging exploration illustrates (i) the effect of different levels of prediction on the expected accuracy, (ii) the branching between abstractions at different sites for different abstractors, (iii) the dependence of the rates on the chemical structure, and (iv) the variation in radical stabilities across chemical families. These results, as well as the demonstrated feasibility of the methodology, should find further utility in the development of accurate rate expressions for arbitrary fuels. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Elliott, Sarah N.↗