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

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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular Structure and Electron Affinity of Metal-Solvent Complexes: Insights from Density Functional Theory Simulations

A molecular level understanding of the structure and energetics of the monovalent and divalent metal ion complexes is of great importance for development of next-generation batteries. Here, Density Functional Theory (DFT) simulations at the ωb97xD/6-31 + G(d,p) level of theory are performed to investigate the interaction of metal ions (Li + , Na + , K + , Mg 2+ , Ca 2+ , Zn 2+ ) with 26 organic solvent molecules. The reduction energetics (electron affinity and reduction potential) and structural responses of the solvent molecules and the molecular complexes are discussed. The DFT calculations are carried out to investigate the structure, energetics and electron affinities of chelated complexes of water (H 2 O), tetrahydrofuran (THF) and di-methoxy ethane (DME) solvent molecules. Additionally, ab initio dynamic simulations (AIMD) at 298 K using atom centered density matrix propagation (ADMP) formalism are performed to understand the spontaneous structure formation upon electron attachment of the metal ion-solvent complexes. The ADMP simulations indicate the decomposition of Mg + -(DME) 3 complex via cleavage of C–O bond of one of the three DME molecules indicating irreversible decomposition of DME in the presence of the Mg + radical. We believe that the data collected as part of this investigation serves as a library of fundamental knowledge towards a deeper understanding of the electrode-electrolyte interfacial reactions.

25 ENERGY STORAGE↗
DOE OSTI2016

Cytotoxicity of Titanate-Calcium Complexes to MC3T3 Osteoblast-Like Cells

Monosodium titanates (MST) are a relatively novel form of particulate titanium dioxide that have been proposed for biological use as metal sorbents or delivery agents, most recently calcium (II). In these roles, the toxicity of the titanate or its metal complex is crucial to its biological utility. The aim of this study was to determine the cytotoxicity of MST and MST-calcium complexes with MC3T3 osteoblast-like cells; MST-Ca(II) complexes could be useful to promote bone formation in various hard tissue applications. MC3T3 cells were exposed to native MST or MST-Ca(II) complexes for 24–72 h. A CellTiter-Blue ® assay was employed to assess the metabolic activity of the cells. The results showed that MST and MST-Ca(II) suppressed MC3T3 metabolic activity significantly in a dose-, time-, and cell-density-dependent fashion. MST-Ca(II) suppressed MC3T3 metabolism in a statistically identical manner as native MST at all concentrations. We concluded that MST and MST-Ca(II) are significantly cytotoxic to MC3T3 cells through a mechanism yet unknown; this is a potential problem to the biological utility of these complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Performance of explicit and IMEX MRI multirate methods on complex reactive flow problems within modern parallel adaptive structured grid frameworks

Large-scale multiphysics simulations are computationally challenging due to the coupling of multiple processes with widely disparate time scales. The advent of exascale computing systems exacerbates these challenges since these systems enable ever-increasing size and complexity. In recent years, there has been renewed interest in developing multirate methods as a means to handle the large range of time scales, as these methods may afford greater accuracy and efficiency than more traditional approaches of using implicit-explicit (IMEX) and low-order operator splitting schemes. However, to date there have been few performance studies that compare different classes of multirate integrators on complex application problems. In this work, we study the performance of several newly developed multirate infinitesimal (MRI) methods, implemented in the SUNDIALS solver package, on two reacting flow model problems built on structured mesh frameworks. The first model revisits prior work on a compressible reacting flow problem with complex chemistry that is implemented using BoxLib but where we now include comparisons between a new explicit MRI scheme with the multirate spectral deferred correction (SDC) methods in the original paper. The second problem uses the same complex chemistry as the first problem, combined with a simplified flow model, but runs at a large spatial scale where explicit methods become infeasible due to stability constraints. Two recently developed IMEX MRI multirate methods are tested. These methods rely on advanced features of the AMReX framework on which the model is built, such as multilevel grids and multilevel preconditioners. The results from these two problems show that MRI multirate methods can offer significant performance benefits on complex multiphysics application problems and that these methods may be combined with advanced spatial discretization to compound the advantages of both.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Relaxation behavior in low-frequency complex conductivity of sands caused by bacterial growth and biofilm formation by Shewanella oneidensis under a high-salinity condition

Complex electrical conductivity is increasingly used to monitor subsurface processes associated with microbial activities because microbial cells mostly have surface charges and thus electrical double layers. Although highly saline environments are frequently encountered in coastal and marine sediments, there are limited data available on the complex conductivity associated with microbial activities under a high-salinity condition. Therefore, we have developed the spectral responses of complex conductivity of sand associated with bacterial growth and biofilm formation under a highly saline condition of approximately 1% salinity and approximately 2 S/m pore water conductivity with an emphasis on relaxation behavior. A column test is performed, in which the model bacteria Shewanella oneidensis MR-1 are stimulated for cell growth and biofilm formation in a sand pack, whereas the complex conductivity is monitored from 0.01 Hz to 10 kHz. The test results indicate that the real conductivity increases in the early stage due to the microbial metabolites and the increased surface conduction with cell growth but soon begin to decrease because of the reduction of charge passages due to bioclogging. However, the imaginary conductivity significantly increases with time, and clear bell-shaped relaxation behaviors are observed with the peak frequency of 0.1–1 Hz, associated with the double-layer polarization of cells and electrically conductive pili and biofilms. The Cole-Cole relaxation model appears to capture such relaxation behaviors well, and the modeling results indicate gradual increases in normalized chargeability and decreases in relaxation time during bacterial growth and biofilm formation in the highly saline condition. Comparison with previous literature confirms that the high-salinity condition further increases the normalized chargeability, whereas it suppresses the phase shift and thus the imaginary conductivity. Our results suggest that the complex conductivity can effectively capture microbial biomass formation in sands under a highly saline condition.

58 GEOSCIENCES↗
DOE OSTI2019

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

Chromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM-associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunopurification with mass spectrometry, we have determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, identifying several cell-type specific subunits. We focused on the CP- and cardiomyocyte (CM)-enriched subunits BAF60c (SMARCD3) and BAF170 (SMARCC2). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, and in CMs their loss results in broadly deregulated cardiac gene expression. BRG1, BAF60c and BAF170 modulate chromatin accessibility, to promote accessibility at activated genes while closing chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition, and BAF170 loss leads to retention of BRG1 at CP-specific sites. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby participates in directing temporal gene expression programs in cardiogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects on Human Non-Small Lung Cancer Cell growth of Cu(II), Au(III) and Re(I) Complexes Containing N-donor Pyridyl Ligands: A Senior Undergraduate Research Project

Hands-on synthetic laboratory experiences are critically important for undergraduate chemistry majors. A senior undergraduate research experience at the College of Wooster is presented in the current work. The inorganic complexes [Cu(phenan) 2 (NO 3 ) 2 ] (1; phenan = phenanthridine) and [Au(phenan)Cl 3 ](2) were prepared by metallation of the phenan ligand in a 1:1 CH 3 OH/CH 2 Cl 2 mixture at room temperature. Complex 1 is a new inorganic coordination compound. The structures were confirmed by X-ray crystallography. Complex 1 reveals a distorted octahedral geometry around the central Cu (II) metal ion. In complex 2, the Au(III) atom exhibits a square planar geometry. In addition, we investigated [Cu(dmeobpy)(H 2 O) 2 ][NO 3 ] 2 (3; dmeobpy = 4,4’-dimethoxy-2,2’-bipyridine), [Cu(bap)(NO 3 ) 2 ](4; bap = 2,6-bis(azaindole)pyridine) and [Re(CO) 3 (dmeobpy)Cl] (5). The cytoxocities of 1-5, phenan, dmeobpy, bap and cisplatin were evaluated against several human non-small cell lung cancer cell lines (NCI-H1975, HCC827, NCI-H460, and NCI-A549). Compound 1 exhibited modest antitumor activity against the HCC827 cell line, with an IC 50 value of 19 µM. Compound 3 exhibits lower cytotoxic activity than 1. Finally, the cytotoxic activity of complex 5 (IC 50 < 11 µM) is significantly greater than 1 and 3 against the H1975 cancer cell line.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

The Fifth Adaptor Protein Complex

Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another. Four distinct AP complexes have been identified, which are present in most eukaryotes. We report the existence of a fifth AP complex, AP-5. Tagged AP-5 localises to a late endosomal compartment in HeLa cells. AP-5 does not associate with clathrin and is insensitive to brefeldin A. Knocking down AP-5 subunits interferes with the trafficking of the cationindependent mannose 6-phosphate receptor and causes the cell to form swollen endosomal structures with emanating tubules. AP-5 subunits can be found in all five eukaryotic supergroups, but they have been co-ordinately lost in many organisms. Concatenated phylogenetic analysis provides robust resolution, for the first time, into the evolutionary order of emergence of the adaptor subunit families, showing AP-3 as the basal complex, followed by AP-5, AP-4, and AP-1 and AP-2. Thus, AP-5 is an evolutionarily ancient complex, which is involved in endosomal sorting, and which has links with hereditary spastic paraplegia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Structures of Coxsackievirus, Rhinovirus, and Poliovirus Polymerase Elongation Complexes Solved by Engineering RNA Mediated Crystal Contacts

RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2–2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight base-pairs of the nascent duplex, a fully prepositioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The use of a mercury biosensor to evaluate the bioavailability of mercury-thiol complexes and mechanisms of mercury uptake in bacteria

We discuss as mercury (Hg) biosensors are sensitive to only intracellular Hg, they are useful in the investigation of Hg uptake mechanisms and the effects of speciation on Hg bioavailability to microbes. In this study, bacterial biosensors were used to evaluate the roles that several transporters such as the glutathione, cystine/cysteine, and Mer transporters play in the uptake of Hg from Hg-thiol complexes by comparing uptake rates in strains with functioning transport systems to strains where these transporters had been knocked out by deletion of key genes. The Hg uptake into the biosensors was quantified based on the intracellular conversion of inorganic mercury (Hg(II)) to elemental mercury (Hg(0)) by the enzyme MerA. It was found that uptake of Hg from Hg-cysteine (Hg(CYS) 2 ) and Hg-glutathione (Hg(GSH) 2 ) complexes occurred at the same rate as that of inorganic complexes of Hg(II) into Escherichia coli strains with and without intact Mer transport systems. However, higher rates of Hg uptake were observed in the strain with a functioning Mer transport system. These results demonstrate that thiol-bound Hg is bioavailable to E. coli and that this bioavailability is higher in Hg-resistant bacteria with a complete Mer system than in non-resistant strains. No difference in the uptake rate of Hg from Hg(GSH) 2 was observed in E. coli strains with or without functioning glutathione transport systems. There was also no difference in uptake rates between a wildtype Bacillus subtilis strain with a functioning cystine/cysteine transport system, and a mutant strain where this transport system had been knocked out. These results cast doubt on the viability of the hypothesis that the entire Hg-thiol complex is taken up into the cell by a thiol transporter. It is more likely that the Hg in the Hg-thiol complex is transferred to a transport protein on the cell membrane and is subsequently internalized.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes

Glyceraldehyde 3-phosphate dehydrogenase or GAPDH is an evolutionarily conserved glycolytic enzyme. It catalyzes the two step oxidative phosphorylation of D-glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate using inorganic phosphate and NAD + as cofactor. GAPDH of Group B Streptococcus is a major virulence factor and a potential vaccine candidate. Moreover, since GAPDH activity is essential for bacterial growth it may serve as a possible drug target. Crystal structures of Group B Streptococcus GAPDH in the apo-form, two different binary complexes and the ternary complex are described here. The two binary complexes contained NAD + bound to 2 (mixed-holo) or 4 (holo) subunits of the tetrameric protein. The structure of the mixed-holo complex reveals the effects of NAD + binding on the conformation of the protein. In the ternary complex, the phosphate group of the substrate was bound to the new Pi site in all four subunits. Comparison with the structure of human GAPDH showed several differences near the adenosyl binding pocket in Group B Streptococcus GAPDH. The structures also reveal at least three surface-exposed areas that differ in amino acid sequence compared to the corresponding areas of human GAPDH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Lesion complexity drives age related cancer susceptibility in human mammary epithelial cells

Exposures to various DNA damaging agents can deregulate a wide array of critical mechanisms that maintain genome integrity. It is unclear how these processes are impacted by one's age at the time of exposure and the complexity of the DNA lesion. To clarify this, we employed radiation as a tool to generate simple and complex lesions in normal primary human mammary epithelial cells derived from women of various ages. We hypothesized that genomic instability in the progeny of older cells exposed to complex damages will be exacerbated by age-associated deterioration in function and accentuate age-related cancer predisposition. Centrosome aberrations and changes in stem cell numbers were examined to assess cancer susceptibility. Our data show that the frequency of centrosome aberrations proportionately increases with age following complex damage causing exposures. However, a dose-dependent increase in stem cell numbers was independent of both age and the nature of the insult. Phospho-protein signatures provide mechanistic clues to signaling networks implicated in these effects. Together these studies suggest that complex damage can threaten the genome stability of the stem cell population in older people. Propagation of this instability is subject to influence by the microenvironment and will ultimately define cancer risk in the older population.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Zinc transport in hydrothermal fluids: On the roles of pressure and sulfur vs. chlorine complexing

Here, we provide an experimental confirmation of the suggestion, based on thermodynamic simulations and extrapolations (Zhong et al. 2015), that Zn is transported in the form of chloride complexes in most shallow hydrothermal systems, while bisulfide complexes become increasingly important in deep hydrothermal systems. We used in situ X-ray absorption spectroscopy (XAS) diamond anvil cell experiments to determine Zn(II) speciation in a 1 m NaHS + 0.2 m HCl solution in contact with sphalerite. XANES data clearly show that Zn coordinates to chloride and/or oxygen ligands from room temperature up to and including 200 C, and then at higher temperatures (≥ 300 C) and pressures (> 2 kbar) changes to complexing with sulfur. Our data confirm that bisulfide complexes become increasingly important at high pressure and temperature, due to an increase in sulfur solubility and to favorable entropy contributions for bisulfide versus chloride complexes.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Scope Complexity Options Risks Excursions (SCORE) Factor Mathematical Description.

The purpose of the Scope, Complexity, Options, Risks, Excursions (SCORE) model is to estimate the relative complexity of design variants of future warhead options, resulting in scores. SCORE factors extend this capability by providing estimates of complexity relative to a base system (i.e., all design options are normalized to one weapon system). First, a clearly defined set of scope elements for a warhead option is established. The complexity of each scope element is estimated by Subject Matter Experts (SMEs), including a level of uncertainty, relative to a specific reference system. When determining factors, complexity estimates for a scope element can be directly tied to the base system or chained together via comparable scope elements in a string of reference systems that ends with the base system. The SCORE analysis process is a growing multi-organizational Nuclear Security Enterprise (NSE) effort, under the management of the NA-12 led Enterprise Modeling and Analysis Consortium (EMAC). Historically, it has provided the data elicitation, integration, and computation needed to support the out-year Life Extension Program (LEP) cost estimates included in the Stockpile Stewardship Management Plan (SSMP).

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2017

Modular fabrication and characterization of complex silicon carbide composite structures Advanced Reactor Technologies (ART) Research Final Report (Feb 2015 – May 2017)

Advanced ceramic materials exhibit properties that enable safety and fuel cycle efficiency improvements in advanced nuclear reactors. In order to fully exploit these desirable properties, new processing techniques are required to produce the complex geometries inherent to nuclear fuel assemblies and support structures. Through this project, the state of complex SiC-SiC composite fabrication for nuclear components has advanced significantly. New methods to produce complex SiC-SiC composite structures have been demonstrated in the form factors needed for in-core structural components in advanced high temperature nuclear reactors. Advanced characterization techniques have been employed to demonstrate that these complex SiC-SiC composite structures provide the strength, toughness and hermeticity required for service in harsh reactor conditions. The complex structures produced in this project represent a significant step forward in leveraging the excellent high temperature strength, resistance to neutron induced damage, and low neutron cross section of silicon carbide in nuclear applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Concept of the Complex Bend

Modern synchrotron lattices follow Multi-­Bend Achromat approach and realize low emittance by arranging small horizontal beta-­function and dispersion in the bends. In this paper we propose another optics solution aimed to reach low emittance by using a lattice element that we named as “Complex Bend”. The Complex Bend corresponds to a strong alternate focusing distributed along the bend so to maintain the beta-function and dispersion oscillating at low values. Comprising the ring lattice out of Complex Bends instead of regular dipoles will minimize the Ң-­function and reduce the horizontal emittance while localizing bending to a small fraction of the storage ring circumference. The latter should help to gain more space for Insertion Devices. In the following, we present the concept of Complex Bend, considerations on the choice of its optimal parameters, as well as, thoughts of its practical realization. This paper gives a snapshot where our current studies stand and does not pretend to be a complete description of the Complex Bend engineering design and integration of this element into a specific ring lattice.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Complex Bend II

We present a new optics solution for the Complex Bend, which offers to substantially reduce the device length by removing the dipole poles. The bending is now realized by shifting the quadrupole poles along the horizontal axis. The ring optics can be stable if a specific condition on the relationship between the shifts of focusing and defocusing poles is satisfied. This condition is described in Section 2 of this Tech note. Section 1 describes general analysis of beam transport in a shifted quadrupole. Section 3 presents a set of parameters for such a ring, assuming that a single cell of the Complex Bend consists of 2 Combined Function dipoles. Section 4 describes more realistic model of a single cell constructed with two quadrupoles shifted off their reference trajectory. Section 5 is dedicated to calculations of synchrotron radiation from Complex Bend poles. Throughout this preprint we will call the QF-D-B-D-QD-D-B-D version as Complex Bend I (CBI) and the QF-D-QD-D version as Complex Bend II (CBII).

36 MATERIALS SCIENCE↗