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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A fivefold UO$_2^{2+}$ node is a path to dodecagonal quasicrystal approximants in coordination polymers [plus supplemental information]

Aperiodic formations continue to focus interest in areas ranging from advanced scientific theories to practical everyday applications. Starting from diverse and tightly bonded intermetallic compounds, this world showed an important breakthrough toward the so-called soft systems of meso/macroscale: liquid crystals, thin films, polymers, proteins, etc. This work opens a route for making bulk quasicrystals (QC) in an unprecedented but very common area, with molecular ligands. Since these systems are, to a large extent, transparent, they extend the possible areas of QC application to previously unreachable corners, e.g., photonics. We combined efficient bridging ligands with uranyl pentagonal bonding centers and, unexpectedly, brought the unique attributes of f-element coordination chemistry to an interdisciplinary area of aperiodic formations. Taking advantage of the planar coordination of uranyl ions, we were able to direct the structure expansion solely in two directions with a characteristic snub square tiling, a predicted but previously unobtainable dodecagonal approximant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division

ABSTRACT Cell elongation and division are essential aspects of the bacterial life cycle that must be coordinated for viability and replication. The impact of misregulation of these processes is not well understood as these systems are often not amenable to traditional genetic manipulation. Recently, we reported on the CenKR two-component system (TCS) in the Gram-negative bacterium Rhodobacter sphaeroides that is genetically tractable, widely conserved in α-proteobacteria, and directly regulates the expression of components crucial for cell elongation and division, including genes encoding subunit of the Tol-Pal complex. In this work, we show that overexpression of cenK results in cell filamentation and chaining. Using cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), we generated high-resolution two-dimensional (2D) images and three-dimensional (3D) volumes of the cell envelope and division septum of wild-type cells and a cenK overexpression strain finding that these morphological changes stem from defects in outer membrane (OM) and peptidoglycan (PG) constriction. By monitoring the localization of Pal, PG biosynthesis, and the bacterial cytoskeletal proteins MreB and FtsZ, we developed a model for how increased CenKR activity leads to changes in cell elongation and division. This model predicts that increased CenKR activity decreases the mobility of Pal, delaying OM constriction, and ultimately disrupting the midcell positioning of MreB and FtsZ and interfering with the spatial regulation of PG synthesis and remodeling. IMPORTANCE By coordinating cell elongation and division, bacteria maintain their shape, support critical envelope functions, and orchestrate division. Regulatory and assembly systems have been implicated in these processes in some well-studied Gram-negative bacteria. However, we lack information on these processes and their conservation across the bacterial phylogeny. In R. sphaeroides and other α-proteobacteria, CenKR is an essential two-component system (TCS) that regulates the expression of genes known or predicted to function in cell envelope biosynthesis, elongation, and/or division. Here, we leverage unique features of CenKR to understand how increasing its activity impacts cell elongation/division and use antibiotics to identify how modulating the activity of this TCS leads to changes in cell morphology. Our results provide new insight into how CenKR activity controls the structure and function of the bacterial envelope, the localization of cell elongation and division machinery, and cellular processes in organisms with importance in health, host-microbe interactions, and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Synthesis, structural characterization and antitumor activity of a Ca(II) coordination polymer based on 4-formyl-1,3-benzenedisulfonate-2-furoic acid hydrazide ligands

A new Ca(II) coordination polymer, ([CaL(H{sub 2}O){sub 4}] · (H{sub 2}O){sub 4}){sub n} (L = 4-formyl-1,3-benzenedisulfonate-2-furoic acid hydrazide) has been prepared by one-pot synthesis method. And it was characterized by elemental analysis, IR and thermal analysis. The result of X-ray single-crystal diffraction analysis shows that the Ca(II) complex molecules form one-dimensional chain structure by the bridging oxygen atoms. The anti-tumor activity of L ligand and the Ca(II) coordination polymer has also been studied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

A three-dimensional coordination polymer based on 1,2,3-triazole-4,5-dicarboxylic acid (H{sub 3}tda): ([Cd{sub 12}(tda){sub 8}(H{sub 2}O){sub 11}] · (H{sub 2}O)6.25){sub n}

The title coordination polymer ([Cd{sub 12}(tda){sub 8}(H{sub 2}O){sub 11}] · (H{sub 2}O){sub 6.25}){sub n} (H{sub 3}tda = 1,2,3-triazole-4,5-dicarboxylic acid), has been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. Complex crystallizes in orthorhombic sp. gr. Pmn2{sub 1} with Z = 4. The Cd{sub 2} unit doublebridged by one carboxylate oxygen atom and two neighboring nitrogen atoms from the tda{sup 3–} ligands are linked by the tda{sup 3–}ligands to lead to the 2D (4,4) network in the ac plane. The almost coplanar Cd{sub 2}(μ{sub 5}-tda){sub 2} unit comprised of two Cd ions double-bridged by two tda{sup 3–} ligands through the neighboring nitrogen atoms is connected with the other four Cd{sub 2}(μ{sub 5}-tda){sub 2} units form the undulating 2D network in the ac plane. The (4,4) networks and undulating 2D networks are alternatively connected along the b axis by the tda{sup 3–} ligands coordinating to the Cd ions to form the 3D framework.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

A Two-Dimensional Coordination Polymer Based on 1,1':4',1''-Terphenyl-2',4,4'',5'-tetracarboxylate

The coordination polymer, [MnL{sub 0.5}(H{sub 2}O)(phen)]{sub n} (H{sub 4}L = 1,1':4',1''-terphenyl-2',4,4'',5'-tetracarboxylic acid, phen = 1,10-phenanthroline), has been solvothermal synthesized and structurally characterized by single-crystal X-ray diffraction. Complex crystallizes in triclinic sp. gr.P1̄ with Z = 2. Two carboxylate oxygen atoms in the central phenyl rings from two μu{sub 6{sup −}}L{sup 4–} ligands doubly-bridge two Mn(II) ions to form the dinuclear Mn{sub 2}(O{sub COO{sup −}}){sub 2} unit. Each dinuclear Mn{sub 2}(O{sub COO{sup −}}){sub 2} unit links four L{sup 4–} ligands and each L{sup 4–}ligand bridges four dinuclear Mn{sub 2}(O{sub COO{sup −}}){sub 2} units to generate a 2D coordination network, which can be rationalized as a binodal (4,4) topological network by considering the dinuclear Mn{sub 2}(O{sub COO{sup −}}){sub 2} units and L{sup 4–} ligands as 4-connected nodes.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Coordinated Platoon Routing in a Metropolitan Network

Platooning vehicles—connected and automated vehicles traveling with small intervehicle distances—use less fuel because of reduced aerodynamic drag. Given a network de- fined by vertex and edge sets and a set of vehicles with origin/destination nodes/times, we model and solve the combinatorial optimization problem of coordinated routing of vehicles in a manner that routes them to their destination on time while using the least amount of fuel. Common approaches decompose the platoon coordination and vehicle routing into separate problems. Our model addresses both problems simultaneously to obtain the best solution. We use modern modeling techniques and constraints implied from analyzing the platoon routing problem to address larger numbers of vehicles and larger networks than previously considered. While the numerical method used is unable to certify optimality for candidate solutions to all networks and parameters considered, we obtain excellent solutions in approximately one minute for much larger networks and vehicle sets than previously considered in the literature.

Larson, Jeffrey↗
DOE OSTI2019

Avoiding Communication in Primal and Dual Block Coordinate Descent Methods

Primal and dual block coordinate descent methods are iterative methods for solving regularized and unregularized optimization problems. Distributed-memory parallel implementations of these methods have become popular in analyzing large machine learning datasets. However, existing implementations communicate at every iteration, which, on modern data center and supercomputing architectures, often dominates the cost of floating-point computation. Recent results on communication-avoiding Krylov subspace methods suggest that large speedups are possible by re-organizing iterative algorithms to avoid communication. We show how applying similar algorithmic transformations can lead to primal and dual block coordinate descent methods that only communicate every $s$ iterations---where $s$ is a tuning parameter---instead of every iteration for the regularized least-squares problem. We show that the communication-avoiding variants reduce the number of synchronizations by a factor of $s$ on distributed-memory parallel machines without altering the convergence rate and attain strong scaling speedups of up to $6.1\times$ over the “standard algorithm" on a Cray XC30 supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Gaussian null coordinates, near-horizon geometry and conserved charges on the horizon of extremal nondilatonic black p-branes

In this paper, we examine the emergence of conserved charges on the horizon of a particular class of extremal nondilatonic black [Formula: see text]-branes (which reduce to extremal dilatonic black holes in [Formula: see text] dimensions upon toroidal compactification) in the presence of a probe massless scalar field in the bulk. This result is achieved by writing the black [Formula: see text]-brane geometry in a Gaussian null coordinate system which allows us to get a nonsingular near-horizon geometry description. We find that the near-horizon geometry is [Formula: see text] and that the [Formula: see text] section has an internal structure which can be seen as a warped product of [Formula: see text] in Gaussian null coordinates. We show that the bulk scalar field satisfying the field equations is expanded in terms of nonnormalizable and normalizable modes, which for certain suitable quantization conditions are well-behaved at the boundary of [Formula: see text] space. Furthermore, we show that picking the normalizable modes results in the existence of conserved quantities on the horizon. We discuss the impact of these conserved quantities in the late-time regime.

Astronomy & Astrophysics↗
DOE OSTI2023

Acoustic Codes in 2D Spherical Coordinate

Finite-difference methods are widely used to simulate infrasound propagation in the atmosphere. Flexibility of finite-difference scheme allows implementation of highly heterogeneous media for sound propagation as well as complex source models for sound generation. While full 3-D finite-difference methods have been utilized for local infrasound propagation with pronounced topography, 2-D modeling approach has been preferred for regional and global propagation as full 3-D methods generally require enormous computational resources. Infrasound propagation is often simulated with a second-order finite difference scheme. This lowest-order finite-difference scheme is robust and straightforward to implement complex boundary conditions, but the solution includes large error with numerical dispersion and dissipation. This large numerical error may make the second-order finite-difference not optimal for long range infrasound propagation modeling as the numerical dispersion degrades the accuracy of the solution unacceptably. Here, we developed a high-order finite-difference solver for long-range infrasound simulation. The high-order scheme is particularly popular for linear wave modeling in aeroacoustics owing to its low-dispersive and low-dissipative behavior. We develop and evaluate a high-order finite difference scheme in 2-D axisymmetric coordinates. The axisymmetry allows to approximate 3-D spherical sound propagation and amplitude attenuation by a 2-D method. AC2Dr is developed to simulate infrasound propagation in realistic atmosphere, but can be used for linear acoustic waves in general materials with background flow. AC2Dr in an axisymmetric coordinates allows for spherical radiation of acoustic waves from compact sources.

Sjogreen, Bjorn↗
DOE OSTI2016

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma

Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell fate specification, cell migration and differentiation. When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes have been implicated in cancer. Studying epigenetic mechanisms in development is challenging because they often regulate multiple cellular processes; therefore, elucidating the primary molecular mechanisms involved can be difficult. Here we explore the role of Brg1 (Smarca4) in retinal development and retinoblastoma in mice using molecular and cellular approaches. Brg1 was found to regulate retinal size by controlling cell cycle length, cell cycle exit and cell survival during development. Brg1 was not required for cell fate specification but was required for photoreceptor differentiation and cell adhesion/polarity programs that contribute to proper retinal lamination during development. The combination of defective cell differentiation and lamination led to retinal degeneration in Brg1-deficient retinae. Despite the hypocellularity, premature cell cycle exit, increased cell death and extended cell cycle length, retinal progenitor cells persisted in Brg1-deficient retinae, making them more susceptible to retinoblastoma. In conclusion, ChIP-Seq analysis suggests that Brg1 might regulate gene expression through multiple mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Utah FORGE: Updated Phase 2C Well Location Coordinates

Utah FORGE has been established to develop, test, and improve the technologies and techniques required to develop EGS-type geothermal resources. Drilling of the first of two deep deviated wells, 16A(78)-32, will begin in the second half of 2020. This well will serve as the injection well for the injection-production well pair that will form the heart of the laboratory. This submission contains an archive of well location data within the Roosevelt Hot Springs geothermal area. An Excel spreadsheet is included containing updated GPS data for Utah FORGE wells drilled during Phase 2C (56-32, 68-32, 78-32). This data was collected over time by the Utah Geological Survey and contains all coordinates collected and the final averaged XY coordinates in both Longitude and Latitude and UTM Zone 12, NAD83. Elevation is also included. GIS shapefiles with well points are provided in the archive.

15 GEOTHERMAL ENERGY↗
DOE OSTI2018

A first principles study of energetics and electronic structural responses of uranium-based coordination polymers to Np incorporation

Abstract Recently developed coordination polymers (CPs) and metal organic frameworks (MOFs) may find applications in areas such as catalysis, hydrogen storage, and heavy metal immobilization. Research on the potential application of actinide-based CPs (An-CP/MOFs) is not as advanced as transition metal-based MOFs. In order to modify their structures necessary for optimizing thermodynamic and electronic properties, here, we described how a specific topology of a particular actinide-based CP or MOF responds to the incorporation of other actinides considering their diverse coordination chemistry associated with the multiple valence states and charge-balancing mechanisms. In this study, we apply a recently developed DFT-based method to determine the relative stability of transuranium incorporated CPs in comparison to their uranium counterpart considering both solid and aqueous state sources and sinks to understand the mechanism and energetics of charge-balanced Np 5+ incorporation into three uranium-based CPs. The calculated Np 5+ +H + incorporation energies for these CPs range from 0.33 to 0.52 eV, depending on the organic linker, when using the solid oxide Np source Np 2 O 5 and U sink UO 3 . Incorporation energies of these CPs using aqueous sources and sinks increase to 2.85–3.14 eV. The thermodynamic and structural analysis in this study aides in determining, why certain MOF topologies and ligands are selective for some actinides and not for others. This means that once this method is extended across a variety of CPs with their respective linker molecules and different actinides, it can be used to identify certain CPs with certain organic ligands being specific for certain actinides. This information can be used to construct CPs for actinide separation. This is the first determination of the electronic structure (band structure, density of states) of these uranium- and transuranium-based CPs which may eventually lead to design CPs with certain optical or catalytic properties. While the reduction of the DFT-determined-bandgap goes from 3.1 eV to 2.4 eV when going from CP1 to CP3, showing the influence of the linker, Np 6+ incorporation reduces the bandgap for CP1 and CP3, while increasing it for CP2. The coupled substitution of U 6+ →Np 5+ +H + reduces the bandgap significantly, but only for CP3.

Chemistry↗
DOE OSTI2018

Synthesis and structural characterization of a series of uranyl-betaine coordination complexes

Abstract Trimethylglycine and betainium class ionic liquids were employed in synthesizing six uranyl-betaine coordination complexes: [(μ 2 -(CH 3 )N 2 C 3 H 3 (CH 2 COO)) 2 (UO 2 (Cl)((CH 3 )N 2 C 3 H 3 (CH 2 COO))) 2 ] 2[N(SO 2 CF 3 ) 2 ] ( 1 ), [K][UO 2 (Cl) 3 ((CH 3 ) 3 NCH 2 COO)] ( 2 ), [(CH 3 ) 3 NCH 2 COOH][UO 2 (Cl) 3 ((CH 3 ) 3 NCH 2 COO)]·H 2 O ( 3 ), [LiUO 2 (μ 2 -(CH 3 ) 3 NCH 2 COO) 4 ] 3[N(SO 2 CF 3 ) 2 ] ( 4 ) {(μ 2 -(CH 3 ) 3 NCH 2 COO)UO 2 (NO 3 ) 2 ((CH 3 ) 3 NCH 2 COO)} 2 UO 2 (NO 3 ) 2 , UO 2 (NO 3 ) 2 (H 2 O) 2 ·H 2 O ( 5 ), and UO 2 (Cl) 2 (H 2 O)(μ 2 -(CH 3 ) 3 NCH 2 COO) ( 6 ). These complexes expound upon the variability of mono carboxyl-functionalized uranyl coordination complexes, providing an enhanced framework for investigations into the structural chemistry of analogous actinyl systems.

Crystallography↗
DOE OSTI2012

Application of the BISON Fuel Performance Code to the FUMEX-III Coordinated Research Project

INL recently participated in FUMEX-III, an International Atomic Energy Agency sponsored fuel modeling Coordinated Research Project. A main purpose of FUMEX-III is to compare code predictions to reliable experimental data. During the same time period, the INL initiated development of a new multidimensional (2D and 3D) multiphysics nuclear fuel performance code called BISON. Interactions with international fuel modeling researchers via FUMEX-III played a significant and important role in the BISON evolution, particularly influencing the selection of material and behavioral models which are now included in the code. BISON's ability to model integral fuel rod behavior did not mature until 2011, thus the only FUMEX-III case considered was the Riso3-GE7 experiment, which includes measurements of rod outer diameter following pellet clad mechanical interaction (PCMI) resulting from a power ramp late in fuel life. BISON comparisons to the Riso3-GE7 final rod diameter measurements are quite reasonable. The INL is very interested in participation in the next Fuel Modeling Coordinated Research Project and would like to see the project initiated as soon as possible.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2013

Incorporation of the HYbrid Coordinate Ocean Model (HYCOM) into the Community Climate System Model (CCSM): Evaluation and Climate Applications (Final Report for DOE Grant DE-FG02-07ER64470)

The primary goal of the project entitled “Incorporation of the HYbrid Coordinate Ocean Model (HYCOM) into the Community Climate System Model (CCSM): Evaluation and Climate Applications” was to systematically investigate the performance of the HYbrid Coordinate Ocean Model (HYCOM) as an alternative oceanic component of the NCAR’s Community Climate System Model (CCSM). We have configured two versions of the fully coupled CCSM3/HYCOM: one with a medium resolution (T42) Community Atmospheric Model (CAM) and the other with higher resolution (T85). We have performed a comprehensive analysis of the 400-year fully coupled CCSM3/HYCOM simulations and compared the results with those from CCSM3/POP and with climatological observations, and also we have performed tuning of critical model parameters, including Smagorinsky viscosity, isopycnal diffusivity, and background vertical diffusivity. The analysis shows that most oceanic features are well represented in the CCSM3/HYCOM. The coupled CCSM3/HYCOM (T42) has been integrated for 400 years, and the results have been archived and transferred to the High Performance Computer in the Florida State Univesity. In the last year, we have made comprehensive diagnostics of the long-term simulations by the comparison with the original CCSM3/POP simulation and with the observations. To gain some understanding of the model biases, the mean climate and modes of climate variability of the two models are compared with observations. The examination includes the Northern and Southern Annular Modes (NAM and SAM), the Pacific-North-American (PNA) pattern, the Atlantic Multidecadal Oscillation (AMO), and the main Southern Ocean SST mode. We also compared the performance of ENSO simulation in the coupled models. This report summarizes the main findings from the comparison of long-term CCSM3/HYCOM and CCSM3/POP simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Hot Coordinate Measuring Machine Technical Specifications and Requirements (U)

The goal of this document is to outline the technical specifications and requirements for a new Hot Coordinate Measuring Machine at TA-55. This document should be used in conjunction with the information provided from TA-55 Hot CMM Location Study and TA-55 Hot CMM Technology Assessment. All three documents will guide the user to the optimal coordinate measuring machine selection.

42 ENGINEERING↗