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DOE OSTI2022

Proposal for a quantum random number generator using coherent light and a non-classical observable

The prototype quantum random number (random bit) generator (QRNG) consists of one photon at a time falling on a 50:50 beam splitter followed by random detection in one or the other output beams due to the irreducible probabilistic nature of quantum mechanics. Due to the difficulties in producing single photons on demand, in practice, pulses of weak coherent (laser) light are used. In this paper, we take a different approach, one that uses moderate coherent light. It is shown that a QRNG can be implemented by performing photon-number parity measurements. For moderate coherent light, the probabilities of obtaining even or odd parity in photon counts are 0.5 each. Photon counting with single-photon resolution can be performed through use of a cascade of beam splitters and single-photon detectors, as was done recently in a photon-number parity-based interferometry experiment involving coherent light. We highlight the point that unlike most quantum-based random number generators, our proposal does not require the use of classical de-biasing algorithms or post-processing of the generated bit sequence.

Gerry, Christopher C.↗

DOE OSTI2014

Joint United States: European Union Theoretical and Practical Course on Molecular Approaches for in situ Biogradation

The Joint United States - European Union Theoretical and Practical Course on Molecular Approaches for in situ Biodegradation was held May 24 through June 7 at The University of Oklahoma. Twenty-four graduate and postgraduate students from both the United States and the European Union attended the course. Nine states and ten European countries were represented. Students were assigned living quarters and laboratory partners to maximize interactions between US and EU participants as well as to mix people with different technical backgrounds together. The students used the latest methods in molecular biology to characterize beneficial microorganisms and genes involved in the biodegradation of pollutants at a nearby landfill as well as an active hydrocarbon-producing site, part of which is undergoing bioremediation. Seminars by distinguished scientists were organized to expose the students to the breadth of the environmental field, including field assay and engineering applications, laboratory scale bioreactors, microbiology, genetics, regulation, pathway analysis, design of recombinant bacteria, and application of the associated techniques to the field. Lectures were given by various OU faculty on the principles behind the techniques to be used in the laboratory. These lectures included troubleshooting hints and encouraged questions and comments from the audience. The laboratory experiments covered chemical, microbiological, and molecular genetic analyses of soils; bioavailability of contaminants; enrichment cultures; gene probing; PCR amplification of known genes and gene families; identification of microbes based traditional and nontraditional approaches, nutritional capabilities, and 16S rRNA sequence; mRNA detection; and enzyme assays. Field trips were made to the USGS landfill field sampling site, and to the Tall Grass Prairie Preserve, a Nature Conservancy site which also featured long-term studies of bioremediation of crude oil and brine spills by one of the Principal Investigators in collaboration with University of Tulsa faculty. The students are expected to bring the methods that they learned back to their laboratories to enrich their own and their colleagues' ability to perform state of the art environmental biotechnology research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Sorption and Transport Behavior of {sup 137}Cs, {sup 90}Sr, and {sup 99}Tc on Geological Media in Radioactive Waste Repository, South Korea - 16112

Sorption experiments and a behavior investigation for the radionuclides {sup 137}Cs, {sup 90}Sr, and {sup 99}Tc were conducted using groundwater and solid materials (mud-stone and sandstone) sampled from the Wolsong low- and intermediate-level radioactive waste repository at Gyeongju, Korea. After experiments involving batch sorption, diffusion, and a flow-through column, distribution coefficients (K{sub d}) of the radionuclides were obtained, and sorption properties for each radionuclide were analyzed. Increasing K{sub d} values were observed in the sequence {sup 137}Cs, {sup 90}Sr, and {sup 99}Tc regardless of the geological media tested. For all sorbing radionuclides, K{sub d} values for the mud-stone were observed to be higher than those for sandstone regardless of the groundwater. These higher K{sub d} values are the result of higher levels of total organic carbon in the mud-stone than were present in the sandstone. In addition, the chlorite, kaolinite, and montmorillonite contents in the mud-stone also were higher than in the sandstone. The mineralogical composition of the solid materials was observed to be important in the sorption of sorbing radionuclides. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2015

Criticality safety analysis of spent fuel storage or handling disposals using burnup credit - loading curve calculation - 14445

MILLENNIUM and REEL SAS Companies have shared their own experience to develop a neutron and criticality calculations chain in order to perform isotopic composition predictions of spent fuel after irradiation in a reactor and criticality analysis of fuel storages taking into account burnup credit. The whole calculation sequence is divided into three steps, all calling SCALE 6.1.2 modules. The first two steps are dedicated to the evaluation of isotopic compositions of burnt fuel. As transport and depletion calculations in three dimensions appears to be way too long for the whole core (about several months), dealing with each fuel assembly one by one is the alternative solution MILLENNIUM and REEL SAS commonly chose to study. Therefore, the first step aims at determining the axial burnup profile of a given fuel assembly using a 3-D model with infinite reflections on lateral axes. The T6-depl sequence of TRITON module coupling KENO-VI and ORIGEN-S was used in this step. Sensitivity studies confirmed that addition of the 8 closest neighbors of the studied fuel assembly in the model has an insignificant impact on the axial burnup profile. However, fuel assemblies in the peripheral zone of the core must be treated separately with a model including the nearest fuel assemblies and the effect of peripheral water. Then, the second phase evaluates the isotopic compositions of each fuel assemblies at the center of the active height with a 2-D model under conservative core conditions. The T-depl sequence of the TRITON module coupling NEWT to ORIGEN-S is called in this step. Each fuel assembly must be studied separately to consider loading pattern changes occurring at each cycle. An infinite model with reflections on lateral axes is used and the closest neighbors of the fuel assembly are limited to 2 pins - which is around the size of the neutrons mean free path in the core. This is an innovative physical trick aiming at compensating for a limited computing power. Finally, isotopic compositions calculated are combined with the axial burnup profile of the first step to extrapolate the concentrations along the whole active length. Data can then be added in any criticality model, such as a spent fuel pit or any disposal handling fuel assemblies. Criticality analyses of burnt fissile material using burnup credit can be managed within a reasonable amount of time, on condition that sufficient proofs of code qualification for the studied range of parameters are provided, especially on fission products isotopic compositions calculation. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm

ABSTRACT Although it is becoming clear that many microbial primary producers can also play a role as organic consumers, we know very little about the metabolic regulation of photoautotroph organic matter consumption. Cyanobacteria in phototrophic biofilms can reuse extracellular organic carbon, but the metabolic drivers of extracellular processes are surprisingly complex. We investigated the metabolic foundations of organic matter reuse by comparing exoproteome composition and incorporation of 13 C-labeled and 15 N-labeled cyanobacterial extracellular organic matter (EOM) in a unicyanobacterial biofilm incubated using different light regimes. In the light and the dark, cyanobacterial direct organic C assimilation accounted for 32% and 43%, respectively, of all organic C assimilation in the community. Under photosynthesis conditions, we measured increased excretion of extracellular polymeric substances (EPS) and proteins involved in micronutrient transport, suggesting that requirements for micronutrients may drive EOM assimilation during daylight hours. This interpretation was supported by photosynthesis inhibition experiments, in which cyanobacteria incorporated N-rich EOM-derived material. In contrast, under dark, C-starved conditions, cyanobacteria incorporated C-rich EOM-derived organic matter, decreased excretion of EPS, and showed an increased abundance of degradative exoproteins, demonstrating the use of the extracellular domain for C storage. Sequence-structure modeling of one of these exoproteins predicted a specific hydrolytic activity that was subsequently detected, confirming increased EOM degradation in the dark. Associated heterotrophic bacteria increased in abundance and upregulated transport proteins under dark relative to light conditions. Taken together, our results indicate that biofilm cyanobacteria are successful competitors for organic C and N and that cyanobacterial nutrient and energy requirements control the use of EOM. IMPORTANCE Cyanobacteria are globally distributed primary producers, and the fate of their fixed C influences microbial biogeochemical cycling. This fate is complicated by cyanobacterial degradation and assimilation of organic matter, but because cyanobacteria are assumed to be poor competitors for organic matter consumption, regulation of this process is not well tested. In mats and biofilms, this is especially relevant because cyanobacteria produce an extensive organic extracellular matrix, providing the community with a rich source of nutrients. Light is a well-known regulator of cyanobacterial metabolism, so we characterized the effects of light availability on the incorporation of organic matter. Using stable isotope tracing at the single-cell level, we quantified photoautotroph assimilation under different metabolic conditions and integrated the results with proteomics to elucidate metabolic status. We found that cyanobacteria effectively compete for organic matter in the light and the dark and that nutrient requirements and community interactions contribute to cycling of extracellular organic matter.

09 BIOMASS FUELS↗

DOE OSTI2021

Photo Doppler Velocimetry and Gamma/Neutron Yield Measurements of Godiva-IV Critical Assembly

The purpose of this experiment was to collect data for a dynamic benchmark of the Godiva-IV burst assembly. Data were taken using two different measurement systems. The gamma & neutron flux was measured using a calibrated, high-dynamic-range scintillator detector, the MHD-240. The measurement will be used to determine the total fission yield and alpha throughout the burst and shutdown sequence of Godiva-IV. The Photon Doppler Velocimetry (PDV) measurement detected the surface motion of the burst assembly as a function of time. The combined data will be used in a multi-physics simulation of the Godiva-IV burst assembly.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Discovery of additional ancient genome duplications in yeasts

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

convergent evolution↗

DOE OSTI2013

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well-recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, acetate amendments initially promoted the growth of metal-reducing Geobacter species followed by the growth of sulfate-reducers, as previously observed. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater prior to the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the amoeboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity, and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

breviata↗

DOE OSTI2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Abstract Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Observational evidence for Criegee intermediate oligomerization reactions relevant to aerosol formation in the troposphere

Criegee intermediates are reactive intermediates that are implicated in transforming the composition of Earth’s troposphere and in the formation of secondary organic aerosol, impacting Earth’s radiation balance, air quality and human health. Yet, direct identification of their signatures in the field remains elusive. Here, from particulate and gas-phase mass-spectrometric measurements in the Amazon rainforest, we identify sequences of masses consistent with the expected signatures of oligomerization of the CH 2 OO Criegee intermediate, a process implicated in ozonolysis-driven aerosol formation. In this study, we assess the potential contributions of oligomerization through laboratory ozonolysis experiments, direct kinetic studies of Criegee intermediate reactions, and high-level theoretical calculations. Global atmospheric models built on these kinetics results indicate that Criegee intermediate chemistry may play a larger role in altering the composition of Earth’s troposphere than is captured in current atmospheric models, especially in areas of high humidity. However, the models still capture only a relatively small fraction of the observed signatures, suggesting considerable underestimates of Criegee intermediate concentrations and reactivity and/or the dominance of other, presently uncharacterized, oxidation mechanisms. Resolving the remaining uncertainties in emission inventories and the effects of atmospheric water vapour on key chemical reactions will be required to definitively assess the role of Criegee intermediate oligomerization reactions.

58 GEOSCIENCES↗

DOE OSTI2022

Spiers Memorial Lecture: Theory of unimolecular reactions

One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our ability to model and predict the kinetics of such reactions has grown in leaps and bounds through the synergy of ever more sophisticated experimental studies with increasingly high level theoretical analyses. Herein, this review begins with a brief historical overview of the progress from the Lindemann mechanism to the master equation, which now provides the cornerstone for most theoretical analyses. The current status of ab initio transition state theory based implementations of the master equation is then reviewed, beginning with a discussion of the energy resolved chemical conversion rates, followed by a review of the pressure dependence of the thermal kinetics. The latter discussion focusses on the collisional energy and angular momentum transfer rates as well as the complexities of non-thermal effects and of multiple-well multiple-channel reactions. The synergy with recent state-of-the-art experiments is used to motivate these discussions. Attempts to automate the calculations are also briefly reviewed. Throughout the discussion, we provide our perspective on current understanding and continuing challenges and opportunities. One key challenge relates to the coupling of sequences of reactions, which frequently leads to deviations from the classic presumption of thermal reactants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

16S rRNA squencing to identify microbiomes associated with different crops and different growing conditions

The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers.

16S rRNA sequencing↗

DOE OSTI2013

The Full Scale Seal Experiment - A Seal Industrial Prototype for Cigeo - 13106

The Full Scale Seal (FSS) Experiment is one of various experiments implemented by Andra, within the frame of the Cigeo (the French Deep Geological Repository) Project development, to demonstrate the technical construction feasibility and performance of seals to be constructed, at time of Repository components (shafts, ramps, drifts, disposal vaults) progressive closure. FSS is built inside a drift model fabricated on surface for the purpose. Prior to the scale 1:1 seal construction test, various design tasks are scheduled. They include the engineering work on the drift model to make it fit with the experimental needs, on the various work sequences anticipated for the swelling clay core emplacement and the concrete containment plugs construction, on the specialized handling tools (and installation equipment) manufactured and delivered for the purpose, and of course on the various swelling clay materials and low pH (below 11) concrete formulations developed for the application. The engineering of the 'seal-as-built' commissioning means (tools and methodology) must also be dealt with. The FSS construction experiment is a technological demonstrator, thus it is not focused on the phenomenological survey (and by consequence, on the performance and behaviour forecast). As such, no hydration (forced or natural) is planned. However, the FSS implementation (in particular via the construction and commissioning activities carried out) is a key milestone in view of comforting phenomenological extrapolation in time and scale. The FSS experiment also allows for qualifying the commissioning methods of a real sealing system in the Repository, as built, at time of industrial operations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Evolution of Metastable Phases During Mg Metal Corrosion: An In Situ Cryogenic X-ray Photoelectron Spectroscopy Study

Magnesium and its alloys are potential structural materials candidates for a wide variety of applications due to their high strength-to-weight ratio. However, ductility and poor corrosion resistance under ambient environmental conditions are the bottleneck for industrial deployment. Designing passivation layers and/or corrosion resistant alloys requires fundamental understanding of the corrosion process. The traditional ex-situ spectroscopic measurements of polycrystalline metal surface with ubiquitous surface impurities and grain boundaries only provided an indistinct view of the corrosion process. To clearly distinguish the mechanism and sequence of corrosion process, we employed in-situ cryo-based x-ray photoelectron spectroscopy (XPS) measurements on Mg single crystal surface exposed to aqueous salt solution. Clean Mg (0001) surfaces were exposed to pure D2O and NaCl aqueous solution (5 wt% NaCl+95 wt% D2O). The interfacial reactions were studied using multimodal analysis including XPS, x-ray diffraction (XRD) and scanning electron microscopy (SEM). In contrast to previous studies, our experiments demonstrated the formation of magnesium chloride hydroxide hydrate during aqueous salt corrosion processes. Evidence of metastable ClO* radicals were also found during the initial aqueous salt solution exposure.

Shutthanandan, Vaithiyalingam↗

DOE OSTI2023

Simulation tools, first results and experimental status of the MURAVES experiment

The MUon RAdiography of VESuvius (MURAVES) project aims at the study of Mt. Vesuvius, an active and hazardous volcano near Naples, Italy, with the use of muons freely and abundantly produced by cosmic rays. In particular, the MURAVES experiment intends to perform muographic imaging of the internal structure of the summit of Mt. Vesuvius. The challenging measurement of the rock density distribution in its summit by muography, in conjunction with data from other geophysical techniques, can help model possible eruption dynamics. The MURAVES apparatus consists of an array of three independent and identical muon trackers, with a total sensitive area of 3 square meters. In each tracker, a sequence of 4 XY tracking planes made of plastic scintillators is complemented by a 60 cm thick lead wall inserted between the two downstream planes to improve rejection of background from low energy muons. The apparatus is currently acquiring data. This paper presents preliminary results from the analysis of the first data samples acquired with trackers pointing towards Mt. Vesuvius, including the first relative measurement of the density projection of two flanks of the volcano at three different altitudes; we also present the workflow of the simulation chain of the MURAVES experiment and its ongoing developments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

Sound spectrum of a pulsating optical discharge

A spectrum of sound of an optical discharge generated by a repetitively pulsed (RP) laser radiation has been investigated. The parameters of laser radiation are determined at which the spectrum of sound may contains either many lines, or the main line at the pulse repetition rate and several weaker overtones, or a single line. The spectrum of sound produced by trains of RP radiation comprises the line (and overtones) at the repetition rate of train sequences and the line at the repetition rate of pulses in trains. A CO{sub 2} laser with the pulse repetition rate of f ≈ 3 – 180 kHz and the average power of up to 2 W was used in the experiments. (optical discharges)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗