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214 records · Page 12

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis -element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

59 BASIC BIOLOGICAL SCIENCES↗

Equivalent equilibrium ion distributions in ion sources and beams

Ion sources and ion beams often contain ions of more than one charge-to-mass ratio, due to the presence of multiple ionization states and/or multiple atomic and molecular ion species in the source. We show that, under certain conditions, analysis of these systems can be simplified using the notion of “equivalent equilibrium ion distributions” (EEIDs). These distributions have identical ion trajectories, space-charge distributions, and electric-field distributions, but can be composed of ion species with arbitrary charge-to-mass ratios. We use this result to obtain multi-species generalizations for the perveance of an ion diode, which relates the diode voltage to the extracted beam current, and for the perveance of a drifting ion beam, which determines the axial length-scale for beam expansion due to the self-electric field. Applied to a quasi-neutral plasma ion source containing cold ions and hot electrons, we find that the location of the beam-plasma interface (meniscus), where ions are extracted from the plasma, depends on the electron density and ion energy per unit charge at the interface, independent of the ion composition. For certain types of numerical simulations, EEIDs allow one to calculate the beam optics of an intense multi-species ion source by doing a simulation for a single ion species with an artificial charge-to-mass ratio chosen to minimize computation time. We illustrate these results using the 3D particle-in-cell, finite-element code Aleph. The simulations show how ions in a plasma source self-consistently accelerate to the supersonic speed needed for steady, radially expanding flow. Multi-species equilibria are subject to streaming instabilities because, while the different species have the same kinetic energy per unit charge, their velocities scale with the square root of the charge-to-mass ratio. The simulations show that a strong ion streaming instability can occur in a multi-species plasma ion source.

74 ATOMIC AND MOLECULAR PHYSICS↗

Actinide N-Donor Thermodynamics: Expanding the f-element Covalency Dialogue. Final report

Resolving the chemistry and physics of f-electrons is one of the grand challenges of science for energy technology. A central component of this challenge is describing covalency in actinide-ligand interactions. Crystallography, x-ray spectroscopy and computational techniques have provided reasonable, and in some cases remarkable, support for covalency in actinide-ligand interactions. Courtesy the quality of the results obtained, a significant portion of the covalency dialogue has been forwarded through solid-state and computational studies of the more stable actinides (Th, U, Pu, Np). However; recent reports have questioned whether covalency in actinide interactions increases or decreases across the series. Examination of less-stable trans-actinides (Am, Cm, Bk, Cf and Es) by the aforementioned approaches can be rapidly limited due to material availability, radiological hazards and experimental data to validate computational models. Furthermore, limited thermodynamic data exists to confirm covalency in actinide solution phase interactions that are highly relevant to the remediation and reprocessing of used nuclear fuel. The best-defined interactions of actinides with soft donors in aqueous solutions involve (poly)aminopolycarboxylate (APC) ligands. The chelate effect and binding affinity with the acetic acid APCs subgroups encourages amine interactions with the actinide metal center. In the absence of these factors, amine interactions with actinides are too weak to overcome the protective hydration shell of the dissolved ion. The ability for APCs to force actinide interactions with soft nitrogen donors (as defined by Pearson’s Hard Soft Acid Base theory) encourages the application of these ligands in a variety of processes for actinide recovery from nearly chemically identical lanthanides. The ability to functionalize the amine center of the ligand in a variety of capacities (adding additional amine groups, exchanging the conventional acetate group for an acetate group, etcetera), allows for the APC ligand to serve as a thermodynamic probe for actinide-nitrogen interactions. Perhaps the single most significant breakthrough during the previous funding cycle was the observation that covalency for the transplutonium part of the actinide series can be increasingly influenced with energy degeneracy driven covalency as the actinides become heavier. This was observed most predominantly with dipicolinic acid, but extensions of f-orbital degeneracy were found to affect aliphatic aminopolycarboxylate-actinide complexes through einsteinium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluation of High-Temperature Martensitic Steels for Heavy-Duty Diesel Piston Applications

Five different commercially available high-temperature martensitic steels were evaluated for use in a heavy-duty diesel engine piston application and compared to existing piston alloys 4140 and microalloyed steel 38MnSiVS5 (MAS). Finite element analyses (FEA) were performed to predict the temperature and stress distributions for severe engine operating conditions of interest, and thus aid in the selection of the candidate steels. Complementary material testing was conducted to evaluate the properties relevant to the material performance in a piston. The elevated temperature strength, strength evolution during thermal aging, and thermal property data were used as inputs into the FEA piston models. Additionally, the long-term oxidation performance was assessed relative to the predicted maximum operating temperature for each material using coupon samples in a controlled-atmosphere cyclic-oxidation test rig. A current commercial steel piston alloy, quenched and tempered martensitic steel 4140, was tested in a single-cylinder research engine for a baseline oxidation and mechanical performance assessment using an abbreviated (50h) durability test plan. The predicted suitability of a candidate piston material in an engine is primarily based on its elevated temperature strength, oxidation resistance, and the complex influence of thermal conductivity, the latter of which is substantially lower for the candidate materials considered in this research relative to the traditional alloys. Although the lower thermal conductivity causes the candidate alloys to operate in higher temperature ranges under identical engine operating conditions and piston geometries, increasing the likelihood of partially or completely negating their strength and oxidation resistance advantages relative to 4140 and MAS steels, this evaluation indicates that several of the candidate piston alloys are predicted to enable improved oxidation resistance under more severe engine operating conditions relative to the current piston materials. However, further evaluation is required to determine if the elevated temperature fatigue strength and durability of these alloys are suitable for more severe engine conditions.

36 MATERIALS SCIENCE↗

Understanding the Importance of Labile Fe(III) during Fe(II)-Catalyzed Transformation of Metastable Iron Oxyhydroxides

Transformation of metastable Fe(III) oxyhydroxides is a prominent process in natural environments and can be significantly accelerated by the coexisting aqueous Fe(II) (Fe(II) aq ). Recent evidence points to the solution mass transfer of labile Fe(III) (Fe(III) labile ) as the primary intermediate species of general importance. However, a mechanistic aspect that remains unclear is the dependence of phase outcomes on the identity of the metastable Fe(III) oxyhydroxide precursor. Here, we compared the coupled evolution of Fe(II) species, solid phases, and Fe(III) labile throughout the Fe(II)-catalyzed transformation of lepidocrocite (Lp) versus ferrihydrite (Fh) at equal Fe(III) mass loadings with 0.2–1.0 mM Fe(II) aq at pH = 7.0. Similar to Fh, the conversion of Lp to product phases occurs by a dissolution–reprecipitation mechanism mediated by Fe(III) labile that seeds the nucleation of products. Though for Fh we observed a transformation to goethite (Gt), accompanied by the transient emergence and decline of Lp, for initial Lp we observed magnetite (Mt) as the main product. Further, a linear correlation between the formation rate of Mt and the effective supersaturation in terms of Fe(III) labile concentration shows that Fe(II)-induced transformation of Lp into Mt is governed by the classical nucleation theory. When Lp is replaced by equimolar Gt, Mt formation is suppressed by opening a lower barrier pathway to Gt by heterogeneous nucleation and growth on the added Gt seeds. The collective findings add to the mechanistic understanding of factors governing phase selections that impact iron bioavailability, system redox potential, and the fate and transport of coupled elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A New Plasma Radar Concept for Simultaneous Magnetic and Density Measurements

An innovative, compact 288GHz interferometer has been fabricated, tested, installed and successfully demonstrated on the LAPD-U magnetized plasma at UCLA. The system takes advantage of frequency modulated (FM) radar techniques to deliver a compact heterodyne system. In addition, the reflected power from the source is taken advantage of to eliminate the need for additional quasi-optical components. Electron density in LAPD-U plasma has recently been increased substantially thereby requiring a higher frequency/shorter wavelength interferometer to avoid deleterious refractive effects. This system satisfies those needs. The system uses a 96GHz varactor tuned Gunn oscillator which passes to a passive tripler. This tripler has ~3% conversion efficiency. The 288GHz radiation is then coupled to free space using a so-called dual-mode or Pickett horn. The output 288GHz beam is then coupled to an aspheric lens manufactured from low-loss, high-density polyethylene. This lens is employed to collimate the emerging beam. Small axial adjustment of the lens position can also be used to create a slowly focusing beam so as to optimize the measured signal. In addition, up-down or side-to-side adjustment of the lens can be utilized to steer the beam vertically or horizontally – again to optimize alignment. The propagating beam passes through a beam splitter and then through a water-free, bubble-free fused quartz window into the LAPD-U vacuum vessel. The beam-splitter is a thin sheet of G10 which reflects a small fraction of the incident power (~5 %) towards a zero-bias detector optimized for the frequency range from 220 to 300GHz. Note that waveguides at this frequency have dimensions of ~0.9mm x 0.45mm and so have very large conductive losses. This drives the use of quasi-optical propagation. The detector requires no DC bias and is very responsive (> 1V/mW into 1MΩ). Radiation is coupled to the detector via a similar lens-horn arrangement used for the launch. This reflected beam acts as the local oscillator or reference millimeter-wave beam for the detector. The remainder of the launched source beam then enters the LAPD-U vacuum vessel and passes through the plasma at the mid-plane until reaching the opposing port which is closed off with an aluminum flange. This flange is used as a mirror to retroreflect the incident 288GHz beam back along its path. The retroreflected beam exits the input port but does NOT couple directly into the zero-bias detector. Instead, the majority of the return power continues towards the 288GHz source. As mentioned above the transmitted beam enters the source a second time. This would appear undesirable. However, at these frequencies multipliers are highly non-linear elements which results in a significant portion of the return beam (~20%) re-emerging from the multiplier and horn and then coupling via the G10 beam-splitter to the zero-bias detector. This approach eliminated the need for a second quasi-optical beam-splitter. The system is extremely compact measuring approximately 28 inches x 20 inches. The above did not explain how heterodyne operation was achieved. As mentioned above the Gunn oscillator is able to be varactor tuned. This allows a low voltage to be applied to control the operating frequency of the Gunn oscillator. During heterodyne operation a sawtooth shaped voltage is applied to the varactor at 750kHz using an 80MHz Arbitrary Waveform Generator (AWG). This voltage changes the Gunn frequency linearly during the up-sweep which is then reset abruptly at the sawtooth crash to be immediately followed by another linear sweep. Passage through the 288GHz multiplier triples the frequency change experienced by the electromagnetic wave. These frequency changes are small – tens of megahertz. This FM radar approach results in the launched electromagnetic wave frequencies at the detector for the reference and plasma wave to be different. The approximately 10 ns delay propagation delay for the plasma beam results in the local oscillator and plasma beams NOT having an identical frequency – there is in fact a fixed difference frequency. The frequency tuning level of the Gunn oscillator is then adjusted so that there is ONE cycle of this difference frequency during each linear ramp. During the sawtooth crash or downward re-sweep this one cycle replays in reverse but on a very fast timescale. The process then repeats. Low-pass filtering eliminates the fast re-sweep to leave a pure sine wave heterodyne signal. When the plasma is present it introduces a phase delay in the sine wave (caused by the extremely small Doppler shift resulting from the optical path length change). Of course, to measure this phase change we need a reference. This is simply obtained from an arbitrary waveform generator which provides a synchronized output pulse train which again is low pass filtered to obtain a 750kHz sinusoidal voltage reference for the interferometer. The interferometer was installed on LAPD-U where it has worked reliably and has established that electron densities exceeding 1x10 13 cm -3 are routinely achieved. In addition, the system sensitivity was able to easily observe density fluctuation at frequencies up to 50kHz. FM Radar techniques have enabled a full demonstration of a compact, sensitive, high frequency (288GHz/1mm) heterodyne interferometer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Scalable Interior‐Point Gauss–Newton Method for PDE‐Constrained Optimization With Bound Constraints

Here, we present a scalable approach to solve a class of partial differential equation (PDE)‐constrained optimization problems with bound constraints. This approach utilizes a robust full‐space interior‐point (IP)‐Gauss–Newton optimization method. To cope with the poorly‐conditioned IP‐Gauss–Newton saddle‐point linear systems that need to be solved approximately, once per optimization step, we propose two spectrally related preconditioners. These preconditioners leverage the limited informativeness of data in regularized PDE‐constrained optimization problems. A block Gauss–Seidel preconditioner is proposed for the GMRES‐based solution of the IP‐Gauss–Newton linear systems. It is shown, for a large‐class of PDE‐ and bound‐constrained optimization problems, that the spectrum of the block Gauss–Seidel preconditioned IP‐Gauss–Newton matrix is asymptotically independent of discretization and is not impacted by the ill‐conditioning that notoriously plagues interior‐point methods. We exploit symmetry of the IP‐Gauss–Newton linear systems and propose a regularization and log‐barrier Hessian preconditioner for the preconditioned conjugate gradient (PCG)‐based solution of the equivalent IP‐Gauss–Newton–Schur complement linear systems. The eigenvalues of the block Gauss–Seidel preconditioned IP‐Gauss–Newton matrix, that are not equal to one, are identical to the eigenvalues of the regularization and log‐barrier Hessian preconditioned Schur complement matrix. The scalability of the approach is demonstrated on two example problems. The numerical solution of these optimization problems is shown to require a discretization independent number of IP‐Gauss–Newton linear solves. Furthermore, the linear systems are solved in a discretization and IP ill‐conditioning independent number of preconditioned Krylov subspace iterations. The parallel scalability of the preconditioner, achieved via algebraic multigrid component solvers when applicable, and the aforementioned algorithmic scalability permits a parallel scalable means to compute solutions of a large class of PDE‐ and bound‐constrained problems.

PDE-constrained optimization↗

Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08 T , Bs12 T and Bsc2 T , are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter. The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12 T , purple; others beige to brown), marine salt requirement (Bs12 T , Bsc2 T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08 T and T. turnerae strains) and the ability to respire nitrate (Bs08 T ). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08 T =ATCC TSD-121 T =KCTC 62964 T ), Teredinibacter purpureus sp. nov. (type strain Bs12 T =ATCC TSD-122 T =KCTC 62965 T ) and Teredinibacter franksiae sp. nov. (type strain Bsc2 T =ATCC TSD-123 T =KCTC 62966 T ).

59 BASIC BIOLOGICAL SCIENCES↗

The Novel Charfuel® Coal Refining Process 18 TPD Pilot Plant Project for Co- Producing an Upgraded Coal Product, and Commercially Valuable Co- Products: Area of Interest #3 – Coal Beneficiation Pilot Plant Testing (Final Report)

Operation of Carbon Fuels, LLC’s (“CF”) existing, permitted 18 TPD pilot plant located in Golden, Colorado using two individually ranked (ASTM D 388) coal types (two campaigns), employing the novel Charfuel® coal refining process to produce an upgraded coal product and a number of high-valued organic and inorganic coproducts (for which there presently exists large commercial markets) in order to produce engineering and product data which will then be utilized toward the design of a commercial scale integrated facility (pre-feed document). Carbon Fuels, LLC has developed the Charfuel® Coal Refining Process which refines domestically abundant, raw coal (in the same manner as crude oil is refined) to produce the identical, high value co-products that are refined from crude oil. Thus, gasoline, jet fuel, “green diesel”, fuel oil, and marine fuels, as well as petrochemicals such as benzene, toluene, xylene, and methanol are refined from raw coal using this process. The Charfuel® Coal Refining Process is not a coal conversion process, like pyrolysis, or indirect liquefaction. Nor is it an alternative energy system. Rather it is a coal refining process that has the ability to economically produce products traditionally associated with the refining of crude oil but using only abundant, raw coal as the refinery feed stock. The Charfuel® Coal Refining Process is more economical than crude oil refining and is environmentally benign. Therefore, this value added process yields a return on investment well above 50% for a commercial facility. Furthermore, the Charfuel® process, unlike alternatives such as ethanol and hydrogen, can utilize the existing transportation, delivery, and other petroleum based systems. Hence, there is no need for new engines, pipelines, tankers, or product acceptance. As a result, the profitability of the process is increased. Objectives: (1) Operation of the integrated 18 tpd pilot plant, using two coal types (ranks); (2) Demonstration of process flexibility in being able to produce different products (gas, liquid, and char), as well as determination of operating parameters for identifying scale up criteria for two coal types (ranks); (3) Generation of engineering and design information (process specifications) for use in designing a commercial scale plant (scale-up); (4) Determination of important environmental issues surrounding the process and the products such as fate of trace elements (mercury and other heavy metals) and distributions of SO2, NOx, and CO 2 by analysis of effluent streams; (5) Production of sufficient product to allow reliable commercial economic evaluation of both the refined coal product and the coproducts; and, (6) Assessment of longer-term reliability of unit operations. Period 1: reconfiguration of the 18 TPD plant to meet specific FOA requirements and to qualify the facility for operation; and, Period 2: operation of the 18 TPD plant for two campaigns using two coals types (ranks) which are widely commercially used and abundant - the first being a subbituminous (Powder River Basin (“PRB”)) coal, and the second a bituminous (Illinois #6) coal.

01 COAL, LIGNITE, AND PEAT↗

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MECHANISTIC MULTIPHYSICS MODELING OF CLADDING RUPTURE IN NUCLEAR FUEL RODS DURING LOSS-OF-COOLANT ACCIDENT CONDITIONS

The Loss of Coolant Accident (LOCA) is a design basis accident that is included as part of the safety analysis of nuclear power plants. As the nuclear industry desires to increase the cycle length and discharge burnup of existing nuclear power plants they must demonstrate safe operation during a LOCA on high burnup fuel. During a LOCA transient on high burnup fuel rods, the rods may undergo a process known as fuel fragmentation, relocation, and dispersal (FFRD). To permit dispersal, the cladding encapsulating the fuel must rupture with an opening size large enough to allow the fragmented fuel particles to release. Current licensing tools used by industry and the United States Nuclear Regulatory Commission are limited in geometric fidelity and materials that can be analyzed. These simulation tools generally employ a quasi-two-dimensional (1.5D or Layered1D) or 2D-RZ axisymmetric geometric representations exclusively. While a valid approach under some instances, there are times when important physics have an asymmetric behavior in the fuel rod. Examples include fuel fragmentation, thermal-hydraulic boundary conditions, and cladding rupture, all of which are important for LOCA analysis. As industry pursues burnup extensions it must be demonstrated that fuel dispersal can be mitigated or eliminated. To do this, an understanding of the rupture opening after cladding failure is required. This work presents the development of a model for predicting the size and location of the rupture opening in failed fuel rods during LOCA conditions using advanced modeling and simulation tools. In order to supply the rupture model with appropriate boundary conditions, improvements to fuel fragmentation, axial relocation and oxidation modeling were required. First, the eXtended Finite Element Method (XFEM) is used to mechanistically predict the number of fuel fragments that form due to material strength randomization, criteria for strength randomization, mesh density, power ramping rates and irradiation effects. These predictions with associated uncertainty were compared to empirical correlations developed for UO2 verifying that they can be used with increased confidence in subsequent axial relocation analyses. Secondly, a new first-of-its-kind Layered2D computational framework was developed that provides the ability to apply azimuthally varying boundary conditions while providing discrete layers to track fuel movement during the LOCA. An existing fuel axial relocation model developed for Layered1D was extended to work within the Layered2D framework. A large sensitivity study was performed on the initial version of the model to identify modeling parameters of particular importance, with the emissivity used for radiation after blowdown being the primary source of uncertainty. Then, a simplistic approach to incorporate mechanical degradation of the cladding due to oxidation was also developed to investigate the impact of reduced cladding thickness on predictions of the time to failure of cladding tubes. It was found that the cladding will typically rupture prior to a reduction in thickness that is sufficient to impact the rupture behavior. A model was then developed for predicting cladding rupture that transfers the cladding surface temperatures, rod internal and external pressures, fast neutron fluence, and fast neutron flux from a more detailed Layered1D, Layered2D, or 2D-RZ analysis to a 3D cladding only analysis. Comparisons of the rupture model to a few experiments indicate reasonable predictions. The rupture model was then applied to two accident tolerant fuel concepts (FeCrAl and Cr-coated Zircaloy) where it predicted that both ATF concepts would have smaller rupture openings and delayed rupture times than the standard Zircaloy-4 cladding material under identical loading conditions.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343

Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the identities and functions of many of these gene products have yet to be discovered. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides , forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots. One of these diguanylate cyclases, DGC2884, localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate gene products that may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into the mechanisms of plant association as well as the activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.

59 BASIC BIOLOGICAL SCIENCES↗

Covalency of M–N Bonds in Isomorphous Lanthanide and Actinide 5-(2-Pyridyl)-1H-tetrazolate Complexes

Experimental and computational analyses of [M(pdtz) 3 (H 2 O) 3 ]·3.5H 2 O (M 3+ = Pu 3+ −Cm 3+ , La 3+ −Nd 3+ , and Sm 3+ −Ho 3+ , pdtz− = 5-(2-pyridyl)-1H-tetrazolate) were conducted to understand potential differences in bonding between lanthanide and actinide complexes with a N-donor ligand. Structural analyses show that the An−N bond distances in the Pu 3+ , Am 3+ , and Cm 3+ complexes are within error of one another. Whereas in the lanthanide series, there is a nearly linear decrease in the Ln−N bond lengths from La 3+ to Ho 3+ (excluding Pm 3+ ). The An−N bond lengths are ∼0.015 Å shorter than their similarly-sized lanthanide analogs, in agreement with computational results that suggest greater covalent character in these bonds versus those with lanthanides. QTAIM analysis indicates that the An−N orbital mixing remains essentially unchanged from Pu 3+ to Cm 3+ , consistent with the nearly identical An−N bond lengths. However, upon deconvolution of the NLMOs into orbital compositions, the metal orbital contributions to An−N bonding decreases slightly overall wherein the 6d involvement remains constant, 7s involvement slightly increases, and 5f participation decreases. The molecular orbital energy diagram indicates that energy degeneracy between the 5f metal and 2p ligand orbitals increases from Pu 3+ to Cm 3+ and counteracts the contraction of the 5f orbtials. Together with prior reports of decreasing energy degeneracy between 5f and 3p orbitals from Np 3+ to Cf 3+ , these observations provide guidance on understanding how chemical bonding evolves in the actinide series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge Transport in Zirconium-Based Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are a class of crystalline porous materials characterized by inorganic nodes and multitopic organic linkers. Because of their molecular-scale porosity and periodic intraframework chemical functionality, MOFs are attractive scaffolds for supporting and/or organizing catalysts, photocatalysts, chemical-sensing elements, small enzymes, and numerous other functional-property-imparting, nanometer-scale objects. Notably, these objects can be installed after the synthesis of the MOF, eliminating the need for chemical and thermal compatibility of the objects with the synthesis milieu. Thus, postsynthetically functionalized MOFs can present three-dimensional arrays of high-density, yet well-separated, active sites. Depending on the application and corresponding morphological requirements, MOF materials can be prepared in thin-film form, pelletized form, isolated single-crystal form, polycrystalline powder form, mixed-matrix membrane form, or other forms. For certain applications, most obviously catalytic hydrolysis and electro- or photocatalytic water splitting, but also many others, an additional requirement is water stability. MOFs featuring hexa-zirconium(IV)-oxy nodes satisfy this requirement. For applications involving electrocatalysis, charge storage, photoelectrochemical energy conversion, and chemiresistive sensing, a further requirement is electrical conductivity, as embodied in electron or hole transport. As most MOFs, under most conditions, are electrically insulating, imparting controllable charge-transport behavior is both a chemically intriguing and chemically compelling challenge. Herein, we describe three strategies to render zirconium-based metal–organic frameworks (MOFs) tunably electrically conductive and, therefore, capable of transporting charge on the few nanometers (i.e., several molecular units) to few micrometers (i.e., typical dimensions for MOF microcrystallites) scale. The first strategy centers on redox-hopping between periodically arranged, chemically equivalent sites, essentially repetitive electron (or hole) self-exchange. Zirconium nodes are electrically insulating, but they can function as grafting sites for (a) redox-active inorganic clusters or (b) molecular redox couples. Alternatively, charge hopping based on linker redox properties can be exploited. Marcus’s theory of electron transfer has proven useful for understanding/predicting trends in redox-hopping based conductivity, most notably, in accounting for variations as great as 3000-fold depending on the direction of charge propagation through structurally anisotropic MOFs. In MOF environments, propagation of electronic charge via redox hopping is necessarily accompanied by movement of charge-compensating ions. Consequently, rates of redox hopping can depend on both the identity and concentration of ions permeating the MOF. In the context of electrocatalysis, an important goal is to transport electronic charge fast enough to match or exceed the inherent activity of MOF-based or MOF-immobilized catalysts. Bandlike electronic conductivity is the focus of an alternative strategy: one based on the introduction of molecular guests capable of forming donor–acceptor charge transfer complexes with the host framework. Theory again can be applied predictively to alter conductivity. A third strategy similarly emphasizes electronic conductivity, but it makes use of added bridges in the form of molecular oligomers or inorganic clusters that can then be linked to span the length of a MOF crystallite. For all strategies, retention of molecular-scale porosity is emphasized, as this property is key to many applications. Lastly, while our focus is on Zr-MOFs, the described approaches clearly are extendable to other MOF compositions, as has already been demonstrated, in part, in studies by others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparing light-front quantization with instant-time quantization

Here in this paper we compare light-front quantization and instant-time quantization both at the level of operators and at the level of their Feynman diagram matrix elements. At the level of operators light-front quantization and instant-time quantization lead to equal light-front time commutation (or anticommutation) relations that appear to be quite different from equal instant-time commutation (or anticommutation) relations. Despite this we show that at unequal times instant-time and light-front commutation (or anticommutation) relations actually can be transformed into each other, with it only being the restriction to equal times that makes the commutation (or anticommutation) relations appear to be so different. While our results are valid for both bosons and fermions, for fermions there are subtleties associated with tip of the light cone contributions that need to be taken care of. At the level of Feynman diagrams we show for non-vacuum Feynman diagrams that the pole terms in four-dimensional light-front Feynman diagrams reproduce the widely used three-dimensional light-front on-shell Hamiltonian Fock space formulation in which the light-front energy and light-front momentum are on shell. Moreover, we show that the contributions of pole terms in non-vacuum instant-time and non-vacuum light-front Feynman diagrams are equal. However, because of circle at infinity contributions we show that this equivalence of pole terms fails for four-dimensional light-front vacuum tadpole diagrams. Then, and precisely because of these circle at infinity contributions, we show that light-front vacuum tadpole diagrams are not only nonzero, they quite remarkably are actually equal to the pure pole term instant-time vacuum tadpole diagrams. Light-front vacuum diagrams are not correctly describable by the on-shell Hamiltonian formalism, and thus not by the closely related infinite momentum frame prescription either. Thus for the light-front vacuum sector we must use the off-shell Feynman formalism as it contains information that is not accessible in the on-shell Hamiltonian Fock space approach. We show that light-front quantization is intrinsically nonlocal, and that for fermions this nonlocality is present in Ward identities. One can project fermion spinors into so-called good and bad components, and both of these components contribute in Ward identities. Central to our analysis is that the transformation from instant-time coordinates and fields to light-front coordinates and fields is a unitary, spacetime-dependent translation. Consequently, not only are instant-time quantization and light-front quantization equivalent, because of general coordinate invariance they are unitarily equivalent.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Best Practices for Shielding Analyses of Activated Metals and Spent Resins from Reactor Operation

This report investigated best practices for performing shielding evaluations of Type B waste packages, as defined in 10 CFR Part 71 regulations on packaging and transportation of radioactive material, or packages for which the contents are not defined before loading and may include a broad range of nuclides, geometries, and non-fuel materials. The following non-fuel waste streams were analyzed: Activated metals from decommissioned commercial power reactors, including Type 304 stainless steel, reactor vessel steel, and Inconel, Control blades from boiling water reactors, Neutron-activated corrosion products on surfaces of activated metals, and Spent resins from power plant operations. Measured elemental compositions, including major constituents and impurities, for steel and Inconel samples from commercial power reactors were used in activation calculations to determine radionuclide inventories in activated metals. For a simplified cask model, 60 Co contribution to the total external package dose rate at 30 days after shutdown varied from approximately 60% to 95%, depending on the activated metal, initial cobalt impurity concentration in the metal, and the thickness of the overpack gamma shield. Its maximum contribution to the total external package dose rate of approximately 100% was reached within the time interval of 2 to 5 years after shutdown and was maintained for up to 45 to 60 years after shutdown, depending on material, initial cobalt impurity concentration, and shield thickness. Thereafter, the 60 Co contribution to external package dose rate decreased with increasing decay time. Cobalt-60 is primarily produced by neutron reactions with the cobalt impurity in steel and Inconel. Other important radionuclides in activated metals contributing to package external dose rate are radionuclides with relatively short decay times, including 51 Cr, 59 Fe, 58 Co, and 54 Mn. These radionuclides may be represented as an equivalent 60 Co activity/source because 60 Co gamma ray emissions are bounding in terms of source strength and energy to other important radionuclides identified in the analyzed activated metals. Approaches for modeling the neutron-activated corrosion products that may be attached to activated reactor components were analyzed in this report. It was demonstrated that a surface source is more conservative than a uniform volumetric source for the treatment of neutron-activated corrosion products with respect to external package dose rates. An analysis of the maximum radionuclide loadings reported on spent resins identified the radionuclides 137 Cs, 60 Co, 134 Cs, 65 Zn, and 58 Co as the primary contributors to external package dose rate. For a resin cooled for 3.08 years, the external package dose rate was entirely produced by the reported 137 Cs and 60 Co inventory. The neutron sources from actinides found on spent resins or activated metals produced negligible dose rates and may be ignored in dose rate analyses. Effects of idealized waste material, source geometry, and spatial material/source distributions on external package dose rates were determined based on dose rate results for a simplified cask model under normal conditions of transport. Type 304 stainless steel, zirconium, and aluminum with adjusted mass densities based on a maximum content weight were analyzed for material modeling effects on external package dose rate. These materials produced identical external package dose rates within the statistical uncertainties of the dose rate estimates. Among four different source geometry configurations with homogeneous material of different mass densities, uniform volumetric source distribution, and the same source strength, the geometry configuration with lowest mass density (i.e., minimum self-shielding effect among the four cases) was most conservative. Spatial source distributions that better represent localized peak 60 Co activity values were more conservative than a uniform volumetric source distribution, assuming the same weight and total source strength per package. The increase in external dose rate caused by localized source peaks can be as much as the ratio between source peak activity density to average activity density, depending on the location of the activated metal with peak activity density. Therefore, the shielding analysis may be simplified if localized peak activities and the average activity per package can be measured/determined and documented at the time of cask loading. For simplicity, external package dose rates may be determined based on average source activity and a uniform volumetric source distribution. The dose rate results from that calculation model multiplied by the ratio of peak activity density to average activity density will produce maximum dose rate values for conservative estimates.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗