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Materials Data on La3B(CBr)2 by Materials Project

La3B(CBr)2 crystallizes in the orthorhombic Pnma space group. The structure is three-dimensional. there are three inequivalent La+2.33+ sites. In the first La+2.33+ site, La+2.33+ is bonded to three C4- and three Br1- atoms to form a mixture of distorted edge and corner-sharing LaC3Br3 octahedra. The corner-sharing octahedra tilt angles range from 40–106°. There are one shorter (2.48 Å) and two longer (2.66 Å) La–C bond lengths. There are two shorter (3.12 Å) and one longer (3.39 Å) La–Br bond lengths. In the second La+2.33+ site, La+2.33+ is bonded to three C4- and three equivalent Br1- atoms to form a mixture of distorted edge and corner-sharing LaC3Br3 octahedra. The corner-sharing octahedra tilt angles range from 40–106°. There are one shorter (2.50 Å) and two longer (2.67 Å) La–C bond lengths. There are two shorter (3.19 Å) and one longer (3.43 Å) La–Br bond lengths. In the third La+2.33+ site, La+2.33+ is bonded in a 8-coordinate geometry to four C4- and four Br1- atoms. There are two shorter (2.81 Å) and two longer (2.85 Å) La–C bond lengths. There are a spread of La–Br bond distances ranging from 3.22–3.42 Å. B3+ is bonded in a bent 150 degrees geometry to two C4- atoms. There is one shorter (1.49 Å) and one longer (1.50 Å) B–C bond length. There are two inequivalent C4- sites. In the first C4- site, C4- is bonded in a 1-coordinate geometry to five La+2.33+ and one B3+ atom. In the second C4- site, C4- is bonded in a 1-coordinate geometry to five La+2.33+ and one B3+ atom. There are two inequivalent Br1- sites. In the first Br1- site, Br1- is bonded in a 5-coordinate geometry to five La+2.33+ atoms. In the second Br1- site, Br1- is bonded in a 5-coordinate geometry to five La+2.33+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Ce6B2(CBr)3 by Materials Project

Ce6B2(CBr)3 crystallizes in the monoclinic P2/m space group. The structure is three-dimensional. there are three inequivalent Ce+3.17+ sites. In the first Ce+3.17+ site, Ce+3.17+ is bonded to three C+3.33- and three Br1- atoms to form a mixture of distorted corner and edge-sharing CeC3Br3 octahedra. The corner-sharing octahedral tilt angles are 0°. There are one shorter (2.35 Å) and two longer (2.54 Å) Ce–C bond lengths. There are two shorter (3.16 Å) and one longer (3.17 Å) Ce–Br bond lengths. In the second Ce+3.17+ site, Ce+3.17+ is bonded in a 9-coordinate geometry to four equivalent B3-, two equivalent C+3.33-, and three Br1- atoms. There are two shorter (2.69 Å) and two longer (2.82 Å) Ce–B bond lengths. Both Ce–C bond lengths are 2.55 Å. There are two shorter (3.24 Å) and one longer (3.30 Å) Ce–Br bond lengths. In the third Ce+3.17+ site, Ce+3.17+ is bonded in a 7-coordinate geometry to two equivalent B3-, three C+3.33-, and two equivalent Br1- atoms. Both Ce–B bond lengths are 2.86 Å. There are two shorter (2.57 Å) and one longer (2.59 Å) Ce–C bond lengths. Both Ce–Br bond lengths are 3.16 Å. B3- is bonded in a distorted single-bond geometry to six Ce+3.17+ and one C+3.33- atom. The B–C bond length is 1.53 Å. There are two inequivalent C+3.33- sites. In the first C+3.33- site, C+3.33- is bonded to five Ce+3.17+ and one B3- atom to form distorted edge-sharing CCe5B octahedra. In the second C+3.33- site, C+3.33- is bonded to six Ce+3.17+ atoms to form edge-sharing CCe6 octahedra. There are two inequivalent Br1- sites. In the first Br1- site, Br1- is bonded in a 5-coordinate geometry to five Ce+3.17+ atoms. In the second Br1- site, Br1- is bonded in a 6-coordinate geometry to six Ce+3.17+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on SiH8(CBr)4 by Materials Project

SiH8(CBr)4 is Silicon tetrafluoride-derived structured and crystallizes in the tetragonal P-42_1c space group. The structure is zero-dimensional and consists of two tetrakis(bromomethyl)silane molecules. Si4+ is bonded in a tetrahedral geometry to four equivalent C2- atoms. All Si–C bond lengths are 1.89 Å. C2- is bonded to one Si4+, two H1+, and one Br1- atom to form distorted corner-sharing CSiH2Br tetrahedra. There is one shorter (1.09 Å) and one longer (1.10 Å) C–H bond length. The C–Br bond length is 1.97 Å. There are two inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one C2- atom. In the second H1+ site, H1+ is bonded in a single-bond geometry to one C2- atom. Br1- is bonded in a single-bond geometry to one C2- atom.

36 MATERIALS SCIENCE↗

Attosecond Probing of Coherent Vibrational Dynamics in CBr 4

A coherent vibrational wavepacket is launched and manipulated in the symmetric stretch (a1) mode of CBr 4 , by impulsive stimulated Raman scattering (ISRS) from nonresonant 400 nm laser pump pulses with various peak intensities on the order of tens of 10 12 W/cm 2 . Extreme ultraviolet (XUV) attosecond transient absorption spectroscopy (ATAS) records the wavepacket dynamics as temporal oscillations in XUV absorption energy at the bromine M 4,5 3d 3/2,5/2 edges around 70 eV. The results are augmented by nuclear timedependent Schrödinger equation simulations. Slopes of the (Br 3d 3/2,5/2 ) –1 10a 1 * core-excited state potential energy surface (PES) along the a 1 mode are calculated to be –9.4 eV/Å from restricted open-shell Kohn–Sham calculations. Using analytical relations derived for the small-displacement limit and the calculated slopes of the core-excited state PES, a deeper insight into the vibrational dynamics is obtained by retrieving the experimental excursion amplitude of the vibrational wavepacket and the amount of population transferred to the vibrational first-excited state as a function of pump-pulse peak intensity. Experimentally, the results show that XUV ATAS is capable of resolving oscillations in the XUV absorption energy on the order of a few to tens of meV with tens of femtosecond time precision. This corresponds to change in C–Br bond length on the order of 10 –4 to 10 –3 Å. The results and the analytic relationships offer a clear physical picture, on multiple levels of understanding, of how the pump-pulse peak intensity controls the vibrational dynamics launched by nonresonant ISRS in the small-displacement limit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Materials Data on P2H9(CBr)3 by Materials Project

P(CH3)3PBr3 crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of four phosphorus tribromide molecules and four trimethylphosphine molecules.

36 MATERIALS SCIENCE↗

Materials Data on FePH12(CBr)4 by Materials Project

FeBr4(CH3)4P is Silicon tetrafluoride-derived structured and crystallizes in the cubic F-43m space group. The structure is zero-dimensional and consists of four phosphonium, tetramethyl- molecules and four tetrabromoiron molecules.

36 MATERIALS SCIENCE↗

Chromatin binding by HORMAD proteins regulates meiotic recombination initiation

The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae , the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix–turn–helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced Fuel Cycle Cost Basis Report: Supporting Document 6 A Proposed Methodology for Transformation of Reactor Cost Data to the ‘What-It-Takes’ Table

Note: This document represents work undertaken to refine the CBR approach for arriving at recommended cost values for the reactor sub-modules. This information is provided to indicate the possible direction of evolution in future CBR updates and encourage comments from CBR users. Since this document was developed concurrent with many of the following R-modules, the methodology was applied only in the analysis of the fast reactor (Module R2) data. In future revisions an attempt will be made to use this methodology uniformly.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Biocatalytic system for comparatively assessing the functional association of monolignol cytochrome P450 monooxygenases with their redox partners

Lignin is a complex heterogenous polymer derived from oxidative radical polymerization of three monolignols, i.e., p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. These lignin monomeric precursors structurally differ in their methoxy groups of the benzene rings. In phenylpropanoid-monolignol biosynthetic pathway, the endoplasmic reticulum (ER)-resident cytochrome P450 monooxygenases, cinnamate 4-hydroxylase, coumaroyl ester 3´-hydroxylase and ferulate 5-hydroxylase, establish the key structural characteristics of monolignols. The catalysis of cytochrome P450 monooxygenase requires reducing power, which is supplied by the ER electron transfer chains, composed of cytochrome P450 oxidoreductase (CPR), cytochrome b5 reductase (CBR) and/or cytochrome b5 protein (CB5), from cofactor NADPH or NADH. While NADPH-dependent CPR serves as the typical electron donor for most P450 enzymes, in some cases, the CBR-CB5 or CPR-CB5 electron transfer system also transfers electrons to the terminal P450 enzymes. There are tremendous studies focusing on the discovery and characterization of cytochrome P450 monooxygenases. However, very limited attention has been paid to the versatility and the roles of electron transfer components in the P450 catalytic system. Due to the membrane-residence property of both P450 enzymes and electron transfer components, it is challenging to establish an effective experimental system to evaluate the functional association of P450s with their redox partners. This chapter describes a yeast cell biocatalytic system and the related experimental procedures for comparatively assessing the functional relationship of monolignol biosynthetic P450 enzymes and different redox partners in their catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

Bipartite chromatin recognition by Hop1 from two diverged Holozoa

In meiosis, ploidy reduction is driven by a complex series of DNA breakage and recombination events between homologous chromosomes, orchestrated by meiotic HORMA domain proteins (HORMADs). Meiotic HORMADs possess a central chromatin binding region (CBR) whose architecture varies across eukaryotic groups. Here, we determine high-resolution crystal structures of the meiotic HORMAD CBR from two diverged aquatic Holozoa,Schistosoma mansoniandPatiria miniata, which reveal tightly associated plant homeodomain (PHD) and winged helix-turn-helix (wHTH) domains. We show that PHD–wHTH CBRs bind duplex DNA through their wHTH domains, and identify key residues that disrupt this interaction. Combining experimental and predicted structures, we show that the CBRs’ PHDs likely interact with the tail of histone H3, and may discriminate between unmethylated and trimethylated H3 lysine 4. Finally, we show that Holozoa Hop1 CBRs bind nucleosomes in vitro in a bipartite manner involving both the PHD and wHTH domain. Our data reveal how meiotic HORMADs with PHD–wHTH CBRs can bind chromatin and potentially discriminate between chromatin states to drive meiotic recombination to specific chromosomal regions.

Life Sciences & Biomedicine - Other Topics↗

Two- and three-body fragmentation of multiply charged tribromomethane by ultrafast laser pulses

We investigate the two- and three-body fragmentation of tribromomethane (bromoform, CHBr 3 ) resulting from multiple ionization by 28-femtosecond near-infrared laser pulses with a peak intensity of 6 × 10 14 W cm -2 . The analysis focuses on channels consisting exclusively of ionic fragments, which are measured by coincidence momentum imaging. The dominant two-body fragmentation channel is found to be Br + + CHBr 2 +. Weaker HBr + + CBr 2 +, CHBr + + Br 2 +, CHBr 2+ + Br 2 +, and Br + + CHBr 2 2+ channels, some of which require bond rearrangement prior to or during the fragmentation, are also observed. The dominant three-body fragmentation channel is found to be Br + + Br + + CHBr + . This channel includes both concerted and sequential fragmentation pathways, which we identify using the native frames analysis method. We compare the measured kinetic energy release and momentum correlations with the results of classical Coulomb explosion simulations and discuss the possible isomerization of CHBr 3 to BrCHBr–Br (iso-CHBr 3 ) prior to the fragmentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Arabidopsis cytochrome b 5 proteins support fatty acid ω-3 but not ω-6 desaturation

Fatty acids are primary components of lipids, which serve as major energy sources in cells and play essential roles in membrane structure, signaling, and metabolic regulation (Shanklin and Cahoon 1998). The degree of fatty acid unsaturation critically influences lipid physicochemical properties, thereby affecting membrane fluidity and biological function (Nguyen et al. 2019). In Arabidopsis thaliana, fatty acid desaturation occurs via 2 parallel pathways: the “prokaryotic pathway” in plastids, involving glycosylglycerides, such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and phospholipid phosphatidylglycerol (PG); and the “eukaryotic pathway” in the endoplasmic reticulum (ER), involving phosphatidylcholine (PC) (Lou et al. 2014) (Supplementary Figure S1). Seven fatty acid desaturases (FADs) in Arabidopsis differentially desaturate each glycerolipid class in the plastid and ER (Nguyen et al. 2019). FAD2, an ER-resident ω-6 fatty acid desaturase, catalyzes the conversion of oleic acid (18:1) to linoleic acid (18:2), which can be further desaturated to α-linolenic acid (18:3) by FAD3, an ER-resident ω-3 fatty acid desaturase. In plastids, FAD6 catalyzes the desaturation of 18:1/16:1 to produce 18:2/16:2, while FAD7 and FAD8 redundantly convert 18:2/16:2 to 18:3/16:3 (Li-Beisson et al. 2013; Nguyen et al. 2019). Additionally, fatty acids synthesized in the ER can also be reimported into plastids to their site of de novo synthesis (Xu et al. 2010). All FADs require reducing power, in the form of 2 electrons, for catalysis, but the sources of the electrons vary between their subcellular localizations. In the ER, FAD2 and FAD3 receive electrons from a cytochrome b 5 (CB5)-based electron transfer chain comprising cytochrome b 5 reductase (CBR) and CB5. In contrast, ferredoxin serves as the electron donor for plastid-localized FAD6, FAD7, and FAD8 (Ohlrogge and Browse 1995; Andreu et al. 2007). While the relative contributions of the 2 pathways to total cellular desaturation products vary across tissues and species, most polyunsaturated FA biosynthesis in seeds occurs via ER-resident FAD2 and FAD3 (Miquel and Browse 1992; Ohlrogge and Browse 1995).

59 BASIC BIOLOGICAL SCIENCES↗

K-space algorithmic reconstruction (KAREN): a robust statistical methodology to separate Bragg and diffuse scattering

Diffuse scattering occurring in the Bragg diffraction pattern of a long-range-ordered structure represents local deviation from the governing regular lattice. However, interpreting the real-space structure from the diffraction pattern presents a significant challenge because of the dramatic difference in intensity between the Bragg and diffuse components of the total scattering function. In contrast to the sharp Bragg diffraction, the diffuse signal has generally been considered to be a weak expansive or continuous background signal. In this paper, using 1D and 2D models, it is demonstrated that diffuse scattering in fact consists of a complex array of high-frequency features that must not be averaged into a low-frequency background signal. To evaluate the actual diffuse scattering effectively, an algorithm has been developed that uses robust statistics and traditional signal processing techniques to identify Bragg peaks as signal outliers which can be removed from the overall scattering data and then replaced by statistically valid fill values. This method, described as a 'K-space algorithmic reconstruction' (KAREN), can identify Bragg reflections independent of prior knowledge of a system's unit cell. KAREN does not alter any data other than that in the immediate vicinity of the Bragg reflections, and reconstructs the diffuse component surrounding the Bragg peaks without introducing discontinuities which induce Fourier ripples or artifacts from underfilling `punched' voids. The KAREN algorithm for reconstructing diffuse scattering provides demonstrably better resolution than can be obtained from previously described punch-and-fill methods. The superior structural resolution obtained using the KAREN method is demonstrated by evaluating the complex ordered diffuse scattering observed from the neutron diffraction of a single plastic crystal of CBr 4 using pair distribution function analysis.

36 MATERIALS SCIENCE↗

Tissue-preferential recruitment of electron transfer chains for cytochrome P450-catalyzed phenolic biosynthesis

Cytochrome P450 system consists of P450 monooxygenase and redox pattern(s). While the importance of monooxygenases in plant metabolism is well documented, the metabolic roles of the related redox components have been largely overlooked. Here, we show that distinct electron transfer chains are recruited in phenylpropanoid-monolignol P450 systems to support the synthesis of different classes of phenolics in different plant tissues. While Arabidopsis cinnamate 4-hydroxylase adopts conventional NADPH-cytochrome P450 oxidoreductase (CPR) electron transfer chain for its para-hydroxylation, ferulate 5-hydroxylase employs both NADPH-CPR cytochrome b 5 (CB5) and NADH-cytochrome b 5 reductase (CBR)-CB5 chains to support benzene ring 5-hydroxylation. Moreover, the former route is primarily recruited in the stem for syringyl lignin synthesis, while the latter dominates in the syntheses of 5-hydroxylated phenolics in seeds and seed coat suberin. The availability of reductants NADPH and NADH and the catalytic properties of both reductases to CB5 contribute to the tissue-preferential recruitment of electron transfer systems. Our study unveils an additional layer of complexity and versatility of P450 system that the higher plants evolved for diversifying phenolic repertoires.

59 BASIC BIOLOGICAL SCIENCES↗

Urban-Scale Processes in High-Spatial-Resolution Earth System Models

Cities and their associated urban areas have a much larger impact on the environment than their spatial footprint on the Earth's surface. This is undoubtedly true at local and regional scales, but also at global scales. At this time, more than half of the world's population lives in urban areas (80% in the United States), and the global proportion is projected to climb to 70% by 2050. Therefore, numerical models to study physics, chemistry, and biology affecting the Earth system at regional and global scales must represent the effects of urban areas on climate and the effects of a changing climate on urban areas. At the same time, it is essential to develop state of the art, simple and accurate urban models to better understand the relevant processes and also to address issues related to urban security against the spectra of chemical, biological and radiological (CBR) hazards. Towards bringing urban scientific communities together, a two-and-a-half-day international workshop was held at the Argonne National Laboratory (ANL) in the Chicago area on May 22-24, 2019. This workshop brought together more than 60 national and international experts to develop a roadmap for a better understanding of the issues associated with urban areas and at enhancing the capabilities of regional and global Earth System models (ESMs) in representing the atmospheric dynamics and chemistry, unique aspects of the biosphere and land use, and human dimensions of the urban environment.

54 ENVIRONMENTAL SCIENCES↗

2018 Report on Rare Plant Monitoring and Restoration at the Lawrence Livermore National Laboratory’s Experimental Test Site (Site 300)

This document meets the reporting requirements of LLNL’s California Endangered Species Act Scientific, Educational, or Management Permit (No. 2081 (a)-15-005-RP) for 2018. Section A describes monitoring and field activities conducted by LLNL biologists at the Site 300 native and experimental populations and the Carnegie Canyon native population of the federally-endangered plant, Amsinckia grandiflora (the large-flowered fiddleneck), between January 2018 and December 2018. In addition, monitoring and field activities conducted by LLNL biologists at the Site 300 native populations of the rare plants Eschscholzia rhombipetala (the diamond-petaled California poppy) and Blepharizonia plumosa (the big tarplant) between January 2018 and December 2018 are described in Sections B and C, respectively. Both plants have a California Rare Plant Rank (CRPR) of 1B, which includes species that are rare or endangered throughout their range. California macrophylla (the round-leaved filaree), formerly had a CRPR of 1B, but was downgraded to CBR (Considered But Rejected) in December 2017, as the species was “too common statewide: counties that contain small, localized populations under severe threat should track C. macrophylla as a species of local concern” (California Native Plant Society, 2018). As C. macrophylla is widespread at Site 300 (Carlsen and Paterson, 2018), 2018 will be the final year of monitoring C. macrophylla at Site 300, the results of which are described in Section D. Monitoring of the Navarretia nigelliformis ssp. radians (adobe navarretia), a CRPR 1B species, is planned, and results will be included in future reports.

54 ENVIRONMENTAL SCIENCES↗

Advanced Fuel Cycle Cost Basis Report: Module D1-7 Contact-Handled Pelletized Pressurized Heavy Water (PHWR) UOX Fuel Fabrication (Rev.1)

In addition to literature-based pressurized heavy-water reactor (PHWR) fuel price information in the 2017 AFC-CBR, the what-it-takes (WIT) unit cost data in this update is informed by new analysis and escalation of the 1978 PHWR-UOX fuel life cycle cost (LCC) data from ORNL reports prepared for the 1977–1980 Nonproliferation Alternative Systems Assessment Program (NASAP). (These reports are referenced and summarized in detail in Module D1-PR.) The PHWR fuel fabrication LCC data in these reports is scaled from a bottom-up cost estimate for a reference technology pressurized-water reactor (PWR)—uranium oxide (UOX) fuel fabrication plant by using algorithms that consider the manufacturing process complexity, fuel design complexity, plant floor space requirements, and the radiation and health, safety, and environmental (HS&E) regulatory environment of PHWR-UOX fuel production vis-à-vis light-water reactor (LWR)-UOX production (PWR fuel in this case). The module name has been changed from “Canadian Deuterium Uranium (CANDU)” to the more generic PHWR fuel fabrication in recognition that not all power reactors that might use this fuel type are considered. Unfortunately, the detailed algorithms and their design bases were not archived at the end of the NASAP effort of the commercial CANDU concept specifically developed in the middle of the last century by Atomic Energy of Canada Limited (AECL).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Advanced Fuel Cycle Cost Basis Report: Module D1-1: Uranium-based Ceramic LWR Fuel Fabrication (Rev.2)

Cost module on LWR fuel fabrication to accompany the Advanced Fuel Cycle Cost Basis Report. In this update, we are adding detailed life cycle cost data and a calculated, levelized fabrication cost derived from a non-proprietary bottom-up estimate prepared in 1978 by Oak Ridge National Laboratory (ORNL) (Judkins and Olsen 1978a). In 2018, the 1978 ORNL estimate was escalated by SA&I authors to 2017 USD using factors that represent inflation, escalation above inflation typical of nuclear projects, and the effects of more stringent safety and environmental regulations. In this FY-21 document, the $/kgU results in 2017 USD from the unpublished 2018 interim study (Williams and Ganda 2018) can be escalated to 2020 USD using a factor of 1.052. The literature-based unit cost (or price) data from previous (2004–2017) AFC-CBRs are escalated to 2020 USD using factors from Chapter 8 of the main FY-21 AFC-CBR document. This data, in addition to the results of the updated bottom-up estimate, are used to define the “what-it-takes” (WIT) range for the unit fabrication costs for conventional ceramic UOX light-water reactor (LWR) fuel. This FY-23 document also includes calculated unit costs for accident-tolerant LWR fuels (ATFs) of three different types. Some of these fuels constitute a ceramic pelletized form with fuel meat uranium compounds other than UO2 (a.k.a.,. UOX), thus the change in the title of this module in which the word “UO2” is changed to “Uranium-based Ceramic.”

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗