Weak nanoscale chaos and anomalous relaxation in DNA.

PubMed

Mazur, Alexey K

2017-06-01

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.

PubMed

Schimelman, Jacob B; Dryden, Daniel M; Poudel, Lokendra; Krawiec, Katherine E; Ma, Yingfang; Podgornik, Rudolf; Parsegian, V Adrian; Denoyer, Linda K; Ching, Wai-Yim; Steinmetz, Nicole F; French, Roger H

2015-02-14

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure.

PubMed

Curtiss, W C; Vournakis, J N

1984-01-01

Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.

Configurations of base-pair complexes in solutions. [nucleotide chemistry

NASA Technical Reports Server (NTRS)

Egan, J. T.; Nir, S.; Rein, R.; Macelroy, R.

1978-01-01

A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations

PubMed Central

Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu

2017-01-01

We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861

The influence of arene-ring size on stacking interaction with canonical base pairs

NASA Astrophysics Data System (ADS)

Formánek, Martin; Burda, Jaroslav V.

2014-04-01

Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson-Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

The Importance of Electron Correlation on Stacking Interaction of Adenine-Thymine Base-Pair Step in B-DNA: A Quantum Monte Carlo Study.

PubMed

Hongo, Kenta; Cuong, Nguyen Thanh; Maezono, Ryo

2013-02-12

We report fixed-node diffusion Monte Carlo (DMC) calculations of stacking interaction energy between two adenine(A)-thymine(T) base pairs in B-DNA (AA:TT), for which reference data are available, obtained from a complete basis set estimate of CCSD(T) (coupled-cluster with singles, doubles, and perturbative triples). We consider four sets of nodal surfaces obtained from self-consistent field calculations and examine how the different nodal surfaces affect the DMC potential energy curves of the AA:TT molecule and the resulting stacking energies. We find that the DMC potential energy curves using the different nodes look similar to each other as a whole. We also benchmark the performance of various quantum chemistry methods, including Hartree-Fock (HF) theory, second-order Møller-Plesset perturbation theory (MP2), and density functional theory (DFT). The DMC and recently developed DFT results of the stacking energy reasonably agree with the reference, while the HF, MP2, and conventional DFT methods give unsatisfactory results.

The Weak Lensing Masses of Filaments between Luminous Red Galaxies

NASA Astrophysics Data System (ADS)

Epps, Seth D.; Hudson, Michael J.

2017-07-01

In the standard model of non-linear structure formation, a cosmic web of dark-matter-dominated filaments connects dark matter haloes. In this paper, we stack the weak lensing signal of an ensemble of filaments between groups and clusters of galaxies. Specifically, we detect the weak lensing signal, using CFHTLenS galaxy ellipticities, from stacked filaments between Sloan Digital Sky Survey (SDSS)-III/Baryon Oscillation Spectroscopic Survey luminous red galaxies (LRGs). As a control, we compare the physical LRG pairs with projected LRG pairs that are more widely separated in redshift space. We detect the excess filament mass density in the projected pairs at the 5σ level, finding a mass of (1.6 ± 0.3) × 1013 M⊙ for a stacked filament region 7.1 h-1 Mpc long and 2.5 h-1 Mpc wide. This filament signal is compared with a model based on the three-point galaxy-galaxy-convergence correlation function, as developed in Clampitt et al., yielding reasonable agreement.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Talukder, Srijeeta; Sen, Shrabani; Chaudhury, Pinaki, E-mail: pinakc@rediffmail.com

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stackingmore » interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.« less

Lightweight bipolar storage battery

NASA Technical Reports Server (NTRS)

Rowlette, John J. (Inventor)

1992-01-01

An apparatus [10] is disclosed for a lightweight bipolar battery of the end-plate cell stack design. Current flow through a bipolar cell stack [12] is collected by a pair of copper end-plates [16a,16b] and transferred edgewise out of the battery by a pair of lightweight, low resistance copper terminals [28a,28b]. The copper terminals parallel the surface of a corresponding copper end-plate [16a,16b] to maximize battery throughput. The bipolar cell stack [12], copper end-plates [16a,16b] and copper terminals [28a,28b] are rigidly sandwiched between a pair of nonconductive rigid end-plates [20] having a lightweight fiber honeycomb core which eliminates distortion of individual plates within the bipolar cell stack due to internal pressures. Insulating foam [30] is injected into the fiber honeycomb core to reduce heat transfer into and out of the bipolar cell stack and to maintain uniform cell performance. A sealed battery enclosure [ 22] exposes a pair of terminal ends [26a,26b] for connection with an external circuit.

Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside-nucleoside pair.

PubMed

Bag, Subhendu Sekhar; Talukdar, Sangita; Kundu, Rajen; Saito, Isao; Jana, Subhashis

2014-01-25

Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

NASA Astrophysics Data System (ADS)

Yusufaly, Tahir; Olson, Wilma; Li, Yun

2014-03-01

Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ``opening'' mode and two shear ``sliding'' and ``tearing'' modes in the orthogonal plane. The stacking interactions of the methyl groups are observed to globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. The results have implications for the epigenetic control of DNA mechanics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Shuangluo; Vashishtha, Ashwani; Bulkley, David

During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold dependingmore » on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.« less

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

PubMed

Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

2015-04-01

The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

Thin-Film Coated Plastic Wrap for Food Packaging

PubMed Central

Wu, Hsin-Yu; Liu, Ting-Xuan; Hsu, Chia-Hsun; Cho, Yun-Shao; Xu, Zhi-Jia; Liao, Shu-Chuan; Zeng, Bo-Han; Jiang, Yeu-Long; Lien, Shui-Yang

2017-01-01

In this study, the antimicrobial property and food package capability of polymethylpentene (PMP) substrate with silicon oxdie (SiOx) and organic silicon (SiCxHy) stacked layers deposited by an inductively coupled plasma chemical vapor deposition system were investigated. The experimental results show that the stacked pair number of SiOx/SiCxHy on PMP is limited to three pairs, beyond which the films will crack and cause package failure. The three-pair SiOx/SiCxHy on PMP shows a low water vapor transmission rate of 0.57 g/m2/day and a high water contact angle of 102°. Three-pair thin-film coated PMP demonstrates no microbe adhesion and exhibits antibacterial properties within 24 h. Food shelf life testing performed at 28 °C and 80% humidity reports that the three-pair thin-film coated PMP can enhance the food shelf-life to 120 h. The results indicate that the silicon-based thin film may be a promising material for antibacterial food packaging applications to extend the shelf-life of food products. PMID:28773178

Fuel cell stack with internal manifolds for reactant gases

DOEpatents

Schnacke, Arthur W.

1985-01-01

A fuel cell stack includes a plurality of plate-like fuel cells arranged along an axis generally parallel to cell thickness with electrically conductive separator plates between each pair of cells. A plurality of axial manifolds are provided at opposite sides of the stack in outer marginal portions beyond the edges of electrodes and electrolyte tiles. Sealing rings prevent cross-leakage of oxidant fuel gases through use of pairs of outwardly extending lips from opposite tile surfaces bonded to first and second electrode frames respectively. The frames provide transition between electrode edges and manifold perimeters. The pairs of extension lips are sealingly bonded together through an electrically insulative sealing ring with wedge shaped fastening members.

Fuel cell stack with internal manifolds for reactant gases

DOEpatents

Schnacke, A.W.

1983-10-12

A fuel cell stack includes a plurality of plate-like fuel cells arranged along an axis generally parallel to cell thickness with electrically conductive separator plates between each pair of cells. A plurality of axial manifolds are provided at opposite sides of the stack in outer marginal portions beyond the edges of electrodes and electrolyte tiles. Sealing rings prevent cross-leakage of oxidant fuel gases through use of pairs of outwardly extending lips from opposite tile surfaces bonded to first and second electrode frames respectively. The frames provide transition between electrode edges and manifold perimeters. The pairs of extension lips are sealingly bonded together through an electrically insulative sealing ring with wedge shaped fastening members.

Ab initio study of naphtho-homologated DNA bases.

PubMed

Vazquez-Mayagoita, Alvaro; Huertas, Oscar; Fuentes-Cabrera, Miguel; Sumpter, Bobby G; Orozco, Modesto; Luque, F Javier

2008-02-21

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

Estimates of electronic coupling for excess electron transfer in DNA

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.

2005-07-01

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31G* and extended 6-31++G** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules

PubMed Central

Nakano, Shu-ichi; Uotani, Yuuki; Sato, Yuichi; Oka, Hirohito; Fujii, Masayuki; Sugimoto, Naoki

2013-01-01

DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2′-deoxyadenosine and 2′-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2′-deoxycytidine lesions form the base pair with guanine while the 2′-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides. PMID:23873956

Design and fabrication of silver-hydrogen cells

NASA Technical Reports Server (NTRS)

Klein, M. G.

1975-01-01

The design and fabrication of silver-hydrogen secondary cells capable of delivering higher energy densities than comparable nickel-cadmium and nickel-hydrogen cells and relatively high cycle life is presented. An experimental task utilizing single electrode pairs for the optimization of the individual electrode components, the preparation of a design for lightweight 20Ahr cells, and the fabrication of four 20Ahr cells in heavy wall test housing containing electrode stacks of the lightweight design are described. The design approach is based on the use of a single cylindrical self-contained cell with a stacked disc sequence of electrodes. The electrode stack design is based on the use of NASA- Astropower Separator Material, PPF fuel cell anodes, an intercell electrolyte reservoir concept and sintered silver electrodes. Results of performance tests are given.

Solution structure of a GAAA tetraloop receptor RNA.

PubMed Central

Butcher, S E; Dieckmann, T; Feigon, J

1997-01-01

The GAAA tetraloop receptor is an 11-nucleotide RNA sequence that participates in the tertiary folding of a variety of large catalytic RNAs by providing a specific binding site for GAAA tetraloops. Here we report the solution structure of the isolated tetraloop receptor as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. The internal loop of the tetraloop receptor has three adenosines stacked in a cross-strand or zipper-like fashion. This arrangement produces a high degree of base stacking within the asymmetric internal loop without extrahelical bases or kinking the helix. Additional interactions within the internal loop include a U. U mismatch pair and a G.U wobble pair. A comparison with the crystal structure of the receptor RNA bound to its tetraloop shows that a conformational change has to occur upon tetraloop binding, which is in good agreement with previous biochemical data. A model for an alternative binding site within the receptor is proposed based on the NMR structure, phylogenetic data and previous crystallographic structures of tetraloop interactions. PMID:9405377

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

PubMed

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

PubMed Central

Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

2003-01-01

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirouac, Kevin N.; Ling, Hong; UWO)

Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP andmore » dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.« less

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

PubMed

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the Klenow fragment, and the lesser role of shape selection in insertion by pol eta due to its more open and less constrained active site.

Benchmark studies on the building blocks of DNA. 3. Watson-Crick and stacked base pairs.

PubMed

Szalay, Péter G; Watson, Thomas; Perera, Ajith; Lotrich, Victor; Bartlett, Rodney J

2013-04-18

Excited states of stacked adenine-thymine and guanine-cytosine pairs as well as the Watson-Crick pair of guanine-thymine have been investigated using the equation of motion coupled-cluster (EOM-CC) method with single and double as well as approximate triple excitations. Transitions have been assigned, and the form of the excitations has been analyzed. The majority of the excitations could be classified as localized on the nucleobases, but for all three studied systems, charge-transfer (CT) transitions could also be identified. The main aim of this study was to compare the performance of lower-level methods (ADC(2) and TDDFT) to the high-level EOM-CC ones. It was shown that both ADC(2) and TDDFT with long-range correction have nonsystematic error in excitation energies, causing alternation of the energetic ordering of the excitations. Considering the high costs of the EOM-CC calculations, there is a need for reliable new approximate methods.

Ab initio Study of Naptho-Homologated DNA Bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumpter, Bobby G; Vazquez-Mayagoitia, Alvaro; Huertas, Oscar

2008-01-01

Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crickmore » pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.« less

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent.

PubMed

Zhang, Yuyuan; de La Harpe, Kimberly; Hariharan, Mahesh; Kohler, Bern

2018-04-17

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2;#8242;-deoxyadenosine:dT Base Pairing in DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowal, Ewa A.; Ganguly, Manjori; Pallan, Pradeep S.

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 {angstrom} resolution in the presence of Mg{sup 2+}. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry andmore » the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.« less

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2′-deoxyadenosine:dT Base Pairing in DNA

PubMed Central

2011-01-01

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2′-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson–Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C–H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 Å resolution in the presence of Mg2+. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA. PMID:22059929

Synthesis and Properties of Size-expanded DNAs: Toward Designed, Functional Genetic Systems

PubMed Central

Krueger, Andrew T.; Lu, Haige; Lee, Alex H. F.; Kool, Eric T.

2008-01-01

We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA (“expanded DNA”) and yDNA (“wide DNA”). The large component bases are fluorescent, and they display high stacking affinity. When singly substituted into natural DNA, they are destabilizing because the benzo-expanded base pair size is too large for the natural helix. However, when all base pairs are expanded, xDNA and yDNA form highly stable, sequence-selective double helices. The size-expanded DNAs are candidates for components of new, functioning genetic systems. In addition, the fluorescence of expanded DNA bases makes them potentially useful in probing nucleic acids. PMID:17309194

Crystal structure of a four-stranded intercalated DNA: d(C4)

NASA Technical Reports Server (NTRS)

Chen, L.; Cai, L.; Zhang, X.; Rich, A.

1994-01-01

The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

3D-Subspace-Based Auto-Paired Azimuth Angle, Elevation Angle, and Range Estimation for 24G FMCW Radar with an L-Shaped Array

PubMed Central

Nam, HyungSoo; Choi, ByungGil; Oh, Daegun

2018-01-01

In this paper, a three-dimensional (3D)-subspace-based azimuth angle, elevation angle, and range estimation method with auto-pairing is proposed for frequency-modulated continuous waveform (FMCW) radar with an L-shaped array. The proposed method is designed to exploit the 3D shift-invariant structure of the stacked Hankel snapshot matrix for auto-paired azimuth angle, elevation angle, and range estimation. The effectiveness of the proposed method is verified through a variety of experiments conducted in a chamber. For the realization of the proposed method, K-band FMCW radar is implemented with an L-shaped antenna. PMID:29621193

Energetics, Ion and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA.

PubMed

Carr, Carolyn E; Khutsishvili, Irine; Marky, Luis A

2018-06-22

Triplex formation occurs via interaction of a third strand with the major groove of double stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of poly(rA)•poly(rU) (Duplex) and poly(rA)•2poly(rU) (Triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, ΔnNa+ = 0.15 mol Na+/mol base-pair (Duplex) and 0.30 mol Na+/mole base-triplet (Triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, ΔnW = 2 mol H2O/mol base-pair (Duplex unfolding into single strands) and an uptake of structural water, ΔnW = 2 mol H2O/mole base-pair (Triplex unfolding into Duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the ΔV values obtained for the unfolding of Triplex into Duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The ΔV values obtained for the unfolding of Duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.

Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.

PubMed

Nonin, S; Leroy, J L

1996-08-23

At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.

Effective fragment potential study of the interaction of DNA bases.

PubMed

Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

2011-10-20

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.

Manipulative interplay of two adozelesin molecules with d(ATTAAT)₂achieving ligand-stacked Watson-Crick and Hoogsteen base-paired duplex adducts.

PubMed

Hopton, Suzanne R; Thompson, Andrew S

2011-05-17

Previous structural studies of the cyclopropapyrroloindole (CPI) antitumor antibiotics have shown that these ligands bind covalently edge-on into the minor groove of double-stranded DNA. Reversible covalent modification of the DNA via N3 of adenine occurs in a sequence-specific fashion. Early nuclear magnetic resonance and molecular modeling studies with both mono- and bis-alkylating ligands indicated that the ligands fit tightly within the minor groove, causing little distortion of the helix. In this study, we propose a new binding model for several of the CPI-based analogues, in which the aromatic secondary rings form π-stacked complexes within the minor groove. One of the adducts, formed with adozelesin and the d(ATTAAT)(2) sequence, also demonstrates the ability of these ligands to manipulate the DNA of the binding site, resulting in a Hoogsteen base-paired adduct. Although this type of base pairing has been previously observed with the bisfunctional CPI analogue bizelesin, this is the first time that such an observation has been made with a monoalkylating nondimeric analogue. Together, these results provide a new model for the design of CPI-based antitumor antibiotics, which also has a significant bearing on other structurally related and structurally unrelated minor groove-binding ligands. They indicate the dynamic nature of ligand-DNA interactions, demonstrating both DNA conformational flexibility and the ability of two DNA-bound ligands to interact to form stable covalent modified complexes.

Dissociation of single-strand DNA: single-walled carbon nanotube hybrids by Watson-Crick base-pairing.

PubMed

Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

2010-08-18

It has been known that single-strand DNA wraps around a single-walled carbon nanotube (SWNT) by pi-stacking. In this paper it is demonstrated that such DNA is dissociated from the SWNT by Watson-Crick base-pairing with a complementary sequence. Measurement of field effect transistor characteristics indicates a shift of the electrical properties as a result of this "unwrapping" event. We further confirm the suggested process through Raman spectroscopy and gel electrophoresis. Experimental results are verified in view of atomistic mechanisms with molecular dynamics simulations and binding energy analyses.

Control Code for Bearingless Switched-Reluctance Motor

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.

2007-01-01

A computer program has been devised for controlling a machine that is an integral combination of magnetic bearings and a switched-reluctance motor. The motor contains an eight-pole stator and a hybrid rotor, which has both (1) a circular lamination stack for levitation and (2) a six-pole lamination stack for rotation. The program computes drive and levitation currents for the stator windings with real-time feedback control. During normal operation, two of the four pairs of opposing stator poles (each pair at right angles to the other pair) levitate the rotor. The remaining two pairs of stator poles exert torque on the six-pole rotor lamination stack to produce rotation. This version is executable in a control-loop time of 40 s on a Pentium (or equivalent) processor that operates at a clock speed of 400 MHz. The program can be expanded, by addition of logic blocks, to enable control of position along additional axes. The code enables adjustment of operational parameters (e.g., motor speed and stiffness, and damping parameters of magnetic bearings) through computer keyboard key presses.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

The electrostatic characteristics of G·U wobble base pairs

PubMed Central

Xu, Darui; Landon, Theresa; Greenbaum, Nancy L.; Fenley, Marcia O.

2007-01-01

G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. PMID:17526525

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

PubMed

Nonin, S; Phan, A T; Leroy, J L

1997-09-15

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.

Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

PubMed

Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

2018-01-25

Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes

PubMed Central

Watkins, Norman E.; SantaLucia, John

2005-01-01

Nearest-neighbor thermodynamic parameters of the ‘universal pairing base’ deoxyinosine were determined for the pairs I·C, I·A, I·T, I·G and I·I adjacent to G·C and A·T pairs. Ultraviolet absorbance melting curves were measured and non-linear regression performed on 84 oligonucleotide duplexes with 9 or 12 bp lengths. These data were combined with data for 13 inosine containing duplexes from the literature. Multiple linear regression was used to solve for the 32 nearest-neighbor unknowns. The parameters predict the Tm for all sequences within 1.2°C on average. The general trend in decreasing stability is I·C > I·A > I·T ≈ I· G > I·I. The stability trend for the base pair 5′ of the I·X pair is G·C > C·G > A·T > T·A. The stability trend for the base pair 3′ of I·X is the same. These trends indicate a complex interplay between H-bonding, nearest-neighbor stacking, and mismatch geometry. A survey of 14 tandem inosine pairs and 8 tandem self-complementary inosine pairs is also provided. These results may be used in the design of degenerate PCR primers and for degenerate microarray probes. PMID:16264087

Synthetic Spectroscopic Models Related to Coenzymes and Base Pairs, VII. Stacking Interactions in tRNA; the „Bend” at Dimethylguanosine*†

PubMed Central

Iwamura, Hajime; Leonard, Nelson J.; Eisinger, Josef

1970-01-01

We have examined the stacking interactions of N2-dimethyl-guanosine with the nucleosides, e.g., adenosine and cytidine, found adjacent to it in certain tRNA's, by the use of model compounds in which the trimethylene bridge was substituted for the ribose-phosphate-ribose linkage. From the hypochromism exhibited by synthetic 9-[3-(aden-9-yl)propyl]-2-dimethylaminopurine-6-one (IV) and by 9-[3-(cytos-1-yl)propyl]2-dimethylaminopurin-6-one in aqueous solution (VI) it is appearent that the interaction is at least as great between the N2-dimethylguanine moiety and adenine or cytosine as between guanine and these two bases. The fluorescence and phosphorescence emission spectra were obtained in ethylene glycol-water glass at 80°K. The exciplex fluorescence observed for both bi-molecules (IV and VI) containing the N2-dimethylguanine unit provides further evidence for stacked chromophores. PMID:5266146

Sequence periodicity in nucleosomal DNA and intrinsic curvature.

PubMed

Nair, T Murlidharan

2010-05-17

Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

Thermoelectric generator

DOEpatents

Pryslak, N.E.

1974-02-26

A thermoelectric generator having a rigid coupling or stack'' between the heat source and the hot strap joining the thermoelements is described. The stack includes a member of an insulating material, such as ceramic, for electrically isolating the thermoelements from the heat source, and a pair of members of a ductile material, such as gold, one each on each side of the insulating member, to absorb thermal differential expansion stresses in the stack. (Official Gazette)

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Di Felice, Rosa

2011-05-01

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

PubMed

Moreira, Bernardo G; You, Yong; Owczarzy, Richard

2015-03-01

Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

Dual-band absorption of mid-infrared metamaterial absorber based on distinct dielectric spacing layers.

PubMed

Zhang, Nan; Zhou, Peiheng; Cheng, Dengmu; Weng, Xiaolong; Xie, Jianliang; Deng, Longjiang

2013-04-01

We present the simulation, fabrication, and characterization of a dual-band metamaterial absorber in the mid-infrared regime. Two pairs of circular-patterned metal-dielectric stacks are employed to excite the dual-band absorption peaks. Dielectric characteristics of the dielectric spacing layer determine energy dissipation in each resonant stack, i.e., dielectric or ohmic loss. By controlling material parameters, both two mechanisms are introduced into our structure. Up to 98% absorption is obtained at 9.03 and 13.32 μm in the simulation, which is in reasonable agreement with experimental results. The proposed structure holds promise for various applications, e.g., thermal radiation modulators and multicolor infrared focal plane arrays.

Structural and Magnetic Properties of M(mnt)(2) Salts (M = Ni, Pt, Cu) with a Ferrocene-Based Cation, [FcCH(2)N(CH(3))(3)](+). Interplay between M.M and M.S Intermolecular Interactions.

PubMed

Pullen, Anthony E.; Faulmann, Christophe; Pokhodnya, Konstantin I.; Cassoux, Patrick; Tokumoto, Madoka

1998-12-28

A series of metal bis-mnt complexes (mnt = 1,2-dithiolatomaleonitrile) with the trimethylammonium methylferrocene cation have been synthesized and characterized using X-ray diffraction, magnetic susceptibility, and differential scanning calorimetry measurements. The complexes have the formulas (FcCH(2)NMe(3))[Ni(mnt)(2)] (2), (FcCH(2)NMe(3))[Pt(mnt)(2)] (3), and (FcCH(2)NMe(3))(2)[Cu(mnt)(2)] (4) (where Fc = ferrocene). At 300 K, the crystal structures of 1:1 complexes 2 and 3 are very similar. They consist of pairs of [M(mnt)(2)](-) in a slipped configuration packed in stacks. Each [M(mnt)(2)](-) stack is separated from adjacent stacks by two columns of cations. Within the pairs, the [M(mnt)(2)](-) anions interact via short M.S contacts, while there are no short contacts between the pairs. Complex 4, which has a 2:1 stoichiometry, exhibits a markedly different packing arrangement of the anionic units. Due to the special position of the Cu atom in the asymmetric unit cell, [Cu(mnt)(2)](2)(-) dianions are completely isolated from each other. The magnetic susceptibility behavior of the nickel complex is consistent with the presence of magnetically isolated, antiferromagnetically (AF) coupled [Ni(mnt)(2)](-) pairs with the AF exchange parameter, J = -840 cm(-)(1). The platinum complex undergoes an endothermic structural phase transition (T(p)) at 247 K. Below T(p) its structure is characterized by the formation of magnetically isolated [Pt(mnt)(2)](2)(2)(-) dimers in an eclipsed configuration with short Pt.Pt and S.S contacts between monomers. In the magnetic properties, the structural changes reveal themselves as an abrupt susceptibility drop implying a substantial increase of the AF exchange parameter. A mechanism of the phase transition in the platinum compound is proposed. For compound 4, paramagnetic behavior is observed.

Sequence periodicity in nucleosomal DNA and intrinsic curvature

PubMed Central

2010-01-01

Background Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Results Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. Conclusions The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA. PMID:20487515

The Spectral and Environment Properties of z ∼ 2.0–2.5 Quasar Pairs

NASA Astrophysics Data System (ADS)

Lusso, Elisabeta; Fumagalli, Michele; Rafelski, Marc; Neeleman, Marcel; Prochaska, Jason X.; Hennawi, Joseph F.; O’Meara, John M.; Theuns, Tom

2018-06-01

We present the first results from our survey of intervening and proximate Lyman limit systems (LLSs) at z ∼ 2.0–2.5 using the Wide Field Camera 3 on board the Hubble Space Telescope. The quasars in our sample are projected pairs with proper transverse separations R ⊥ ≤ 150 kpc and line-of-sight velocity separations ≲11,000 km s‑1. We construct a stacked ultraviolet (rest-frame wavelengths 700–2000 Å) spectrum of pairs corrected for the intervening Lyman forest and Lyman continuum absorption. The observed spectral composite presents a moderate flux excess for the most prominent broad emission lines, a ∼30% decrease in flux at λ = 800–900 Å compared to a stack of brighter quasars not in pairs at similar redshifts, and lower values of the mean free path of the H I ionizing radiation for pairs ({λ }mfp}912 = 140.7 ± 20.2 {h}70-1 Mpc) compared to single quasars ({λ }mfp}912 = 213.8 ± 28 {h}70-1 Mpc) at the average redshift z ≃ 2.44. From the modeling of LLS absorption in these pairs, we find a higher (∼20%) incidence of proximate LLSs with log {N}{{H}{{I}}} ≥ 17.2 at δv < 5000 km s‑1 compared to single quasars (∼6%). These two rates are different at the 5σ level. Moreover, we find that optically thick absorbers are equally shared between foreground and background quasars. Based on these pieces of evidence, we conclude that there is a moderate excess of gas-absorbing Lyman continuum photons in our closely projected quasar pairs compared to single quasars. We argue that this gas arises mostly within large-scale structures or partially neutral regions inside the dark matter halos where these close pairs reside.

Multi-mJ energy extraction using Yb-fiber based coherent pulse stacking amplification of fs pulses (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ruppe, John M.; Pei, Hanzhang; Chen, Siyun; Sheikhsofla, Morteza; Wilcox, Russell B.; Nees, John A.; Galvanauskas, Almantas

2017-03-01

We report multi-mJ energy (>5mJ) extraction from femtosecond-pulse Yb-doped fiber CPA using coherent pulse stacking amplification (CPSA) technique. This high energy extraction has been enabled by amplifying 10's of nanosecond long pulse sequence, and by using 85-µm core Yb-doped CCC fiber based power amplification stage. The CPSA system consists of 1-GHz repetition rate mode-locked fiber oscillator, followed by a pair of fast phase and amplitude electro-optic modulators, a diffraction-grating based pulse stretcher, a fiber amplifier chain, a GTI-cavity based pulse stacker, and a diffraction grating pulse compressor. Electro-optic modulators are used to carve out from the 1-GHz mode-locked pulse train an amplitude and phase modulated pulse burst, which after stretching and amplification, becomes equal-amplitude pulse burst consisting of 27 stretched pulses, each approximately 1-ns long. Initial pulse-burst shaping accounts for the strong amplifier saturation effects, so that it is compensated at the power amplifier output. This 27-pulse burst is then coherently stacked into a single pulse using a multiplexed sequence of 5 GTI cavities. The compact-footprint 4+1 multiplexed pulse stacker consists of 4 cavities having rountrip of 1 ns, and one Herriott-cell folded cavity - with 9ns roundtrip. After stacking, stretched pulses are compressed down to the bandwidth-limited 300 fs duration using a standard diffraction-grating pulse compressor.

Modeling DNA bubble formation at the atomic scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Correlation and Stacking of Relative Paleointensity and Oxygen Isotope Data

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Channell, J. E.; Lee, D.

2012-12-01

The transformation of a depth-series into a time-series is routinely implemented in the geological sciences. This transformation often involves correlation of a depth-series to an astronomically calibrated time-series. Eyeball tie-points with linear interpolation are still regularly used, although these have the disadvantages of being non-repeatable and not based on firm correlation criteria. Two automated correlation methods are compared: the simulated annealing algorithm (Huybers and Wunsch, 2004) and the Match protocol (Lisiecki and Lisiecki, 2002). Simulated annealing seeks to minimize energy (cross-correlation) as "temperature" is slowly decreased. The Match protocol divides records into intervals, applies penalty functions that constrain accumulation rates, and minimizes the sum of the squares of the differences between two series while maintaining the data sequence in each series. Paired relative paleointensity (RPI) and oxygen isotope records, such as those from IODP Site U1308 and/or reference stacks such as LR04 and PISO, are warped using known warping functions, and then the un-warped and warped time-series are correlated to evaluate the efficiency of the correlation methods. Correlations are performed in tandem to simultaneously optimize RPI and oxygen isotope data. Noise spectra are introduced at differing levels to determine correlation efficiency as noise levels change. A third potential method, known as dynamic time warping, involves minimizing the sum of distances between correlated point pairs across the whole series. A "cost matrix" between the two series is analyzed to find a least-cost path through the matrix. This least-cost path is used to nonlinearly map the time/depth of one record onto the depth/time of another. Dynamic time warping can be expanded to more than two dimensions and used to stack multiple time-series. This procedure can improve on arithmetic stacks, which often lose coherent high-frequency content during the stacking process.

Note: A rigid piezo motor with large output force and an effective method to reduce sliding friction force.

PubMed

Guo, Ying; Hou, Yubin; Lu, Qingyou

2014-05-01

We present a completely practical TunaDrive piezo motor. It consists of a central piezo stack sandwiched by two arm piezo stacks and two leg piezo stacks, respectively, which is then sandwiched and spring-clamped by a pair of parallel polished sapphire rods. It works by alternatively fast expanding and contracting the arm/leg stacks while slowly expanding/contracting the central stack simultaneously. The key point is that sufficiently fast expanding and contracting a limb stack can make its two sliding friction forces well cancel, resulting in the total sliding friction force is <10% of the total static friction force, which can help increase output force greatly. The piezo motor's high compactness, precision, and output force make it perfect in building a high-quality harsh-condition (vibration resistant) atomic resolution scanning probe microscope.

Minimal RED cell pairs markedly improve electrode kinetics and power production in microbial reverse electrodialysis cells.

PubMed

Cusick, Roland D; Hatzell, Marta; Zhang, Fang; Logan, Bruce E

2013-12-17

Power production from microbial reverse electrodialysis cell (MRC) electrodes is substantially improved compared to microbial fuel cells (MFCs) by using ammonium bicarbonate (AmB) solutions in multiple RED cell pair stacks and the cathode chamber. Reducing the number of RED membranes pairs while maintaining enhanced electrode performance could help to reduce capital costs. We show here that using only a single RED cell pair (CP), created by operating the cathode in concentrated AmB, dramatically increased power production normalized to cathode area from both acetate (Acetate: from 0.9 to 3.1 W/m(2)-cat) and wastewater (WW: 0.3 to 1.7 W/m(2)), by reducing solution and charge transfer resistances at the cathode. A second RED cell pair increased RED stack potential and reduced anode charge transfer resistance, further increasing power production (Acetate: 4.2 W/m(2); WW: 1.9 W/m(2)). By maintaining near optimal electrode power production with fewer membranes, power densities normalized to total membrane area for the 1-CP (Acetate: 3.1 W/m(2)-mem; WW: 1.7 W/m(2)) and 2-CP (Acetate: 1.3 W/m(2)-mem; WW: 0.6 W/m(2)) reactors were much higher than previous MRCs (0.3-0.5 W/m(2)-mem with acetate). While operating at peak power, the rate of wastewater COD removal, normalized to reactor volume, was 30-50 times higher in 1-CP and 2-CP MRCs than that in a single chamber MFC. These findings show that even a single cell pair AmB RED stack can significantly enhance electrical power production and wastewater treatment.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

NASA Astrophysics Data System (ADS)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

Design and Applications of Noncanonical DNA Base Pairs.

PubMed

Jissy, A K; Datta, Ayan

2014-01-02

While the Watson-Crick base pairs are known to stabilize the DNA double helix and play a vital role in storage/replication of genetic information, their replacement with non-Watson-Crick base pairs has recently been shown to have interesting practical applications. Nowadays, theoretical calculations are routinely performed on very complex systems to gain a better understanding of how molecules interact with each other. We not only bring together some of the basic concepts of how mispaired or unnatural nucleobases interact with each other but also look at how such an understanding influences the prediction of novel properties and development of new materials. We highlight the recent developments in this field of research. In this Perspective, we discuss the success of DFT methods, particularly, dispersion-corrected DFT, for applications such as pH-controlled molecular switching, electric-field-induced stacking of disk-like molecules with guanine quartets, and optical birefringence of alkali-metal-coordinated guanine quartets. The synergy between theoretical models and real applications is highlighted.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here in this article, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg 2+ appeared during the process of phosphodiester bond formation and was located between the reactingmore » α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.« less

Magnetically-enhanced open string pair production

NASA Astrophysics Data System (ADS)

Lu, J. X.

2017-12-01

We consider the stringy interaction between two parallel stacks of D3 branes placed at a separation. Each stack of D3 branes in a similar fashion carry an electric flux and a magnetic flux with the two sharing no common field strength index. The interaction amplitude has an imaginary part, giving rise to the Schwinger-like pair production of open strings. We find a significantly enhanced rate of this production when the two electric fluxes are almost identical and the brane separation is on the order of string scale. This enhancement will be largest if the two magnetic fluxes are opposite in direction. This novel enhancement results from the interplay of the non-perturbative Schwinger-type pair production due to the electric flux and the stringy tachyon due to the magnetic flux, and may have realistic physical applications.

Solid oxide fuel cell matrix and modules

DOEpatents

Riley, Brian

1990-01-01

Porous refractory ceramic blocks arranged in an abutting, stacked configuration and forming a three dimensional array provide a support structure and coupling means for a plurality of solid oxide fuel cells (SOFCs). Each of the blocks includes a square center channel which forms a vertical shaft when the blocks are arranged in a stacked array. Positioned within the channel is a SOFC unit cell such that a plurality of such SOFC units disposed within a vertical shaft form a string of SOFC units coupled in series. A first pair of facing inner walls of each of the blocks each include an interconnecting channel hole cut horizontally and vertically into the block walls to form gas exit channels. A second pair of facing lateral walls of each block further include a pair of inner half circular grooves which form sleeves to accommodate anode fuel and cathode air tubes. The stack of ceramic blocks is self-supporting, with a plurality of such stacked arrays forming a matrix enclosed in an insulating refractory brick structure having an outer steel layer. The necessary connections for air, fuel, burnt gas, and anode and cathode connections are provided through the brick and steel outer shell. The ceramic blocks are so designed with respect to the strings of modules that by simple and logical design the strings could be replaced by hot reloading if one should fail. The hot reloading concept has not been included in any previous designs.

Note: A rigid piezo motor with large output force and an effective method to reduce sliding friction force

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Ying; Lu, Qingyou, E-mail: qxl@ustc.edu.cn; Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026

2014-05-15

We present a completely practical TunaDrive piezo motor. It consists of a central piezo stack sandwiched by two arm piezo stacks and two leg piezo stacks, respectively, which is then sandwiched and spring-clamped by a pair of parallel polished sapphire rods. It works by alternatively fast expanding and contracting the arm/leg stacks while slowly expanding/contracting the central stack simultaneously. The key point is that sufficiently fast expanding and contracting a limb stack can make its two sliding friction forces well cancel, resulting in the total sliding friction force is <10% of the total static friction force, which can help increasemore » output force greatly. The piezo motor's high compactness, precision, and output force make it perfect in building a high-quality harsh-condition (vibration resistant) atomic resolution scanning probe microscope.« less

Fuel cell system configurations

DOEpatents

Kothmann, Richard E.; Cyphers, Joseph A.

1981-01-01

Fuel cell stack configurations having elongated polygonal cross-sectional shapes and gaskets at the peripheral faces to which flow manifolds are sealingly affixed. Process channels convey a fuel and an oxidant through longer channels, and a cooling fluid is conveyed through relatively shorter cooling passages. The polygonal structure preferably includes at least two right angles, and the faces of the stack are arranged in opposite parallel pairs.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Compact particle accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elizondo-Decanini, Juan M.

2017-08-29

A compact particle accelerator having an input portion configured to receive power to produce particles for acceleration, where the input portion includes a switch, is provided. In a general embodiment, a vacuum tube receives particles produced from the input portion at a first end, and a plurality of wafer stacks are positioned serially along the vacuum tube. Each of the plurality of wafer stacks include a dielectric and metal-oxide pair, wherein each of the plurality of wafer stacks further accelerate the particles in the vacuum tube. A beam shaper coupled to a second end of the vacuum tube shapes themore » particles accelerated by the plurality of wafer stacks into a beam and an output portion outputs the beam.« less

Major Groove Orientation of the (2S)-N6-(2-Hydroxy-3-buten-1-yl)-2′-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene

PubMed Central

2015-01-01

1,3-Butadiene (BD) is an environmental and occupational toxicant classified as a human carcinogen. It is oxidized by cytochrome P450 monooxygenases to 1,2-epoxy-3-butene (EB), which alkylates DNA. BD exposures lead to large numbers of mutations at A:T base pairs even though alkylation of guanines is more prevalent, suggesting that one or more adenine adducts of BD play a role in BD-mediated genotoxicity. However, the etiology of BD-mediated genotoxicity at adenine remains poorly understood. EB alkylates the N6 exocyclic nitrogen of adenine to form N6-(hydroxy-3-buten-1-yl)-2′-dA ((2S)-N6-HB-dA) adducts (TretyakovaN., LinY., SangaiahR., UptonP. B., and SwenbergJ. A. (1997) Carcinogenesis18, 137−1479054600). The structure of the (2S)-N6-HB-dA adduct has been determined in the 5′-d(C1G2G3A4C5Y6A7G8A9A10G11)-3′:5′-d(C12T13T14C15T16T17G18T19 C20C21G22)-3′ duplex [Y = (2S)-N6-HB-dA] containing codon 61 (underlined) of the human N-ras protooncogene, from NMR spectroscopy. The (2S)-N6-HB-dA adduct was positioned in the major groove, such that the butadiene moiety was oriented in the 3′ direction. At the Cα carbon, the methylene protons of the modified nucleobase Y6 faced the 5′ direction, which placed the Cβ carbon in the 3′ direction. The Cβ hydroxyl group faced toward the solvent, as did carbons Cγ and Cδ. The Cβ hydroxyl group did not form hydrogen bonds with either T16O4 or T17O4. The (2S)-N6-HB-dA nucleoside maintained the anti conformation about the glycosyl bond, and the modified base retained Watson–Crick base pairing with the complementary base (T17). The adduct perturbed stacking interactions at base pairs C5:G18, Y6:T17, and A7:T16 such that the Y6 base did not stack with its 5′ neighbor C5, but it did with its 3′ neighbor A7. The complementary thymine T17 stacked well with both 5′ and 3′ neighbors T16 and G18. The presence of the (2S)-N6-HB-dA resulted in a 5 °C reduction in the Tm of the duplex, which is attributed to less favorable stacking interactions and adduct accommodation in the major groove. PMID:25238403

Arsenic sulfide layers for dielectric reflection mirrors prepared from solution

NASA Astrophysics Data System (ADS)

Matějec, Vlastimil; Pedlikova, Jitka; BartoÅ, Ivo; Podrazký, Ondřej

2017-12-01

Chalcogenide materials due to high refractive indices, transparency in the mid-IR spectral region, nonlinear refractive indices, etc, have been employed as fibers and films in different photonic devices such as light amplifiers, optical regenerators, broadband radiation sources. Chalcogenide films can be prepared by physical methods as well as by solution-based techniques in which solutions of chalcogenides in amines are used. This paper presents results on the solution-based fabrication and optical characterization of single arsenic sulfide layers and multilayer stacks containing As2S3 layers together with porous silica layers coated on planar and fiber-optic substrates. Input As2S3 solutions for the layer fabrications were prepared by dissolving As2S3 powder in n-propylamine in a concentration of 0.50 mol/l. These solutions were applied on glass slides by dip-coating method and obtained layers were thermally treated in vacuum at temperatures up to 180 °C. Similar procedure was used for As2S3 layers in multilayer stacks. Such stacks were fabricated by repeating the application of one porous silica layer prepared by the sol-gel method and one As2S3 layer onto glass slides or silica fibers (a diameter of 0.3 mm) by using the dip-coating method. It has been found that the curing process of the applied layers has to be carefully controlled in order to obtain stacks with three pairs of such layers. Single arsenic and porous silica layers were characterized by optical microscopy, and by measuring their transmission spectra in a range of 200-2500 nm. Thicknesses and refractive indices were estimated from the spectra. Transmission spectra of planar multilayer stacks were measured, too. Interference bands have been determined from optical measurements on the multilayer stacks with a minimum transmittance of about 50% which indicates the possibility of using such stacks as reflecting mirrors.

Automated extraction and classification of RNA tertiary structure cyclic motifs

PubMed Central

Lemieux, Sébastien; Major, François

2006-01-01

A minimum cycle basis of the tertiary structure of a large ribosomal subunit (LSU) X-ray crystal structure was analyzed. Most cycles are small, as they are composed of 3- to 5 nt, and repeated across the LSU tertiary structure. We used hierarchical clustering to quantify and classify the 4 nt cycles. One class is defined by the GNRA tetraloop motif. The inspection of the GNRA class revealed peculiar instances in sequence. First is the presence of UA, CA, UC and CC base pairs that substitute the usual sheared GA base pair. Second is the revelation of GNR(Xn)A tetraloops, where Xn is bulged out of the classical GNRA structure, and of GN/RA formed by the two strands of interior-loops. We were able to unambiguously characterize the cycle classes using base stacking and base pairing annotations. The cycles identified correspond to small and cyclic motifs that compose most of the LSU RNA tertiary structure and contribute to its thermodynamic stability. Consequently, the RNA minimum cycles could well be used as the basic elements of RNA tertiary structure prediction methods. PMID:16679452

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oweis, Salah; Chagnon, Guy; Alunans, Peter

An electrochemical cell, including a jelly-roll type electrode stack, and a method for making such cell. The electrochemical cell includes folded electrode portions which form a plane recessed from the end of the electrode stack. The folded electrode portions are preferably formed by making pairs of slits in the electrode end and bending over the electrode portions between each pair of slits. The recessed plane forms a large area to which a current collection tab is subsequently connected. A coating may be applied to the folded portions of the electrode to further increase the contact area with the current collectionmore » tab by eliminating the slight variations in the recessed plane which are due to the overlap of the folded electrode portions.« less

Exploring the Limits of DNA Size: Naphtho-homologated DNA Bases and Pairs

PubMed Central

Lee, Alex H. F.; Kool, Eric T.

2008-01-01

A new design for DNA bases and base pairs is described in which the pyrimidine bases are widened by naphtho-homologation. Two naphtho-homologated deoxyribosides, dyyT (1) and dyyC (2) were synthesized and could be incorporated into oligonucleotides as suitably protected phosphoramidite derivatives. The deoxyribosides were found to be fluorescent, with emission maxima at 446 and 433 nm, respectively. Studies with single substitutions of 1 and 2 in the natural DNA context revealed exceptionally strong base stacking propensity for both. Sequences containing multiple substitutions of 1 and 2 paired opposite adenine and guanine were subsequently mixed and studied by several analytical methods. Data from UV mixing experiments, FRET measurements, fluorescence quenching experiments, and hybridizations on beads suggest that complementary “doublewide DNA” (yyDNA) strands may self-assemble into helical complexes with 1:1 stoichiometry. Data from thermal denaturation plots and CD spectra were less conclusive. Control experiments in one sequence context gave evidence that yyDNA helices, if formed, are preferentially antiparallel and are sequence selective. Hypothesized base pairing schemes are analogous to Watson-Crick pairing, but with glycosidic C1′-C1′ distances widened by over 45%, to ca. 15.2 Å. The possible self-assembly of the double-wide DNA helix establishes a new limit for the size of information-encoding, DNA-like molecules, and the fluorescence of yyDNA bases suggests uses as reporters in monomeric and oligomeric forms. PMID:16834396

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

PubMed Central

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

2017-01-01

Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

On the binding of indeno[1,2-c]isoquinolines in the DNA-topoisomerase I cleavage complex.

PubMed

Xiao, Xiangshu; Antony, Smitha; Pommier, Yves; Cushman, Mark

2005-05-05

An ab initio quantum mechanics calculation is reported which predicts the orientation of indenoisoquinoline 4 in the ternary cleavage complex formed from DNA and topoisomerase I (top1). The results of this calculation are consistent with the hypothetical structures previously proposed for the indenoisoquinoline-DNA-top1 ternary complexes based on molecular modeling, the crystal structure of a recently reported ternary complex, and the biological results obtained with a pair of diaminoalkyl-substituted indenoisoquinoline enantiomers. The results of these studies indicate that the pi-pi stacking interactions between the indenoisoquinolines and the neighboring DNA base pairs play a major role in determining binding orientation. The calculation of the electrostatic potential surface maps of the indenoisoquinolines and the adjacent DNA base pairs shows electrostatic complementarity in the observed binding orientation, leading to the conclusion that electrostatic attraction between the intercalators and the base pairs in the cleavage complex plays a major stabilizing role. On the other hand, the calculation of LUMO and HOMO energies of indenoisoquinoline 13b and neighboring DNA base pairs in conjunction with NBO analysis indicates that charge transfer complex formation plays a relatively minor role in stabilizing the ternary complexes derived from indenoisoquinolines, DNA, and top1. The results of these studies are important in understanding the existing structure-activity relationships for the indenoisoquinolines as top1 inhibitors and as anticancer agents, and they will be important in the future design of indenoisoquinoline-based top1 inhibitors.

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

PubMed Central

Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

2011-01-01

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PMID:20859960

Electronic Interactions of Michler's Ketone with DNA Bases in Synthetic Hairpins.

PubMed

Jalilov, Almaz S; Young, Ryan M; Eaton, Samuel W; Wasielewski, Michael R; Lewis, Frederick D

2015-01-01

The mechanism and dynamics of photoinduced electron transfer in two families of DNA hairpins possessing Michler's ketone linkers have been investigated by means of steady state and time-resolved transient absorption and emission spectroscopies. The excited state behavior of the diol linker employed in hairpin synthesis is similar to that of Michler's ketone in methanol solution. Hairpins possessing only a Michler's ketone linker undergo fast singlet state charge separation and charge recombination with an adjacent purine base, attributed to well-stacked ground state conformations, and intersystem crossing to the triplet state, attributed to poorly stacked ground state conformations. The failure of the triplet to undergo electron transfer reactions on the 7 ns time scale of our measurements is attributed to the low triplet energy and reduction potential of the twisted triplet state. Hairpins possessing both a Michler's ketone linker and a perylenediimide base surrogate separated by four base pairs undergo photoinduced hole transport from the diimide to Michler's ketone upon excitation of the diimide. The efficiency of hole transport is dependent upon the sequence of the intervening purine bases. © 2014 The American Society of Photobiology.

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

DOE PAGES

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John; ...

2015-03-31

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here in this article, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg 2+ appeared during the process of phosphodiester bond formation and was located between the reactingmore » α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.« less

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

PubMed Central

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John; Suo, Zucai

2015-01-01

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5′-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5′-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg2+ appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3′-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion. PMID:25825995

Hydrogen storage and integrated fuel cell assembly

DOEpatents

Gross, Karl J.

2010-08-24

Hydrogen is stored in materials that absorb and desorb hydrogen with temperature dependent rates. A housing is provided that allows for the storage of one or more types of hydrogen-storage materials in close thermal proximity to a fuel cell stack. This arrangement, which includes alternating fuel cell stack and hydrogen-storage units, allows for close thermal matching of the hydrogen storage material and the fuel cell stack. Also, the present invention allows for tailoring of the hydrogen delivery by mixing different materials in one unit. Thermal insulation alternatively allows for a highly efficient unit. Individual power modules including one fuel cell stack surrounded by a pair of hydrogen-storage units allows for distribution of power throughout a vehicle or other electric power consuming devices.

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

NASA Astrophysics Data System (ADS)

Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

2015-03-01

We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

β-Amino acid catalyzed asymmetric Michael additions: design of organocatalysts with catalytic acid/base dyad inspired by serine proteases.

PubMed

Yang, Hui; Wong, Ming Wah

2011-09-16

A new type of chiral β-amino acid catalyst has been computationally designed, mimicking the enzyme catalysis of serine proteases. Our catalyst approach is based on the bioinspired catalytic acid/base dyad, namely, a carboxyl and imidazole pair. DFT calculations predict that this designed organocatalyst catalyzes Michael additions of aldehydes to nitroalkenes with excellent enantioselectivities and remarkably high anti diastereoselectivities. The unusual stacked geometry of the enamine intermediate, hydrogen bonding network, and the adoption of an exo transition state are the keys to understand the stereoselectivity. © 2011 American Chemical Society

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, X.; Patel, D.J.

The authors report on two-dimensional proton NMR studies of echinomycin complexes with the self-complementary d(A1-C2-G3-Tr) and d(T1-C2-G3-A4) duplexes in aqueous solution. The exchangeable and nonexchangeable antibiotic and nucleic acid protons in the 1 echinomycin per tetranucleotide duplex complexes have been assigned from analyses of scalar coupling and distance connectivities in two-dimensional data sets records in H/sub 2/O and D/sub 2/O solution. An analysis of the intermolecular NOE patterns for both complexes combined with large upfield imino proton and large downfield phosphorus complexation chemical shift changes demonstrates that the two quinoxaline chromophores of echinomycin bisintercalate into the minor groove surrounding themore » dC-dG step of each tetranucleotide duplex. Further, the quinoxaline rings selectively stack between A1 and C2 bases in the d(ACGT) complex and between T1 and C2 bases in the d(TCGA) complex. The intermolecular NOE patterns and the base and sugar proton chemical shifts for residues C2 and G3 are virtually identical for the d(ACGT) and d(TCGA) complexes. A large set of intermolecular contacts established from nuclear Overhauser effects (NOEs) between antibiotic and nucleic acid protons in the echinomycin-tetranucleotide complexes in solution are consistent with corresponding contacts reported for echinomycin-oligonucleotide complexes in the crystalline state. The authors demonstrate that the G x G base pairs adopt Watson-Crick pairing in both d(ACGT) and d(TCGA) complexes in solution. By contrast, the A1 x T4 base pairs adopt Hoogsteen pairing for the echinomycin-d(A1-C2-G3-Tr) complex while the T1 x A4 base pairs adopt Watson-Crick pairing for the echinomycin-d(T1-C2-G3-A4) complex in aqueous solution. These results emphasize the role of sequence in discriminating between Watson-Crick and Hoogsteen pairs at base pairs flanking the echinomycin bisintercalation site in solution.« less

Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules.

PubMed

Olsen, Chris M; Shikiya, Ronald; Ganugula, Rajkumar; Reiling-Steffensmeier, Calliste; Khutsishvili, Irine; Johnson, Sarah E; Marky, Luis A

2016-05-01

The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition. Copyright © 2015. Published by Elsevier B.V.

Synaptic behaviors of thin-film transistor with a Pt/HfO x /n-type indium-gallium-zinc oxide gate stack.

PubMed

Yang, Paul; Park, Daehoon; Beom, Keonwon; Kim, Hyung Jun; Kang, Chi Jung; Yoon, Tae-Sik

2018-07-20

We report a variety of synaptic behaviors in a thin-film transistor (TFT) with a metal-oxide-semiconductor gate stack that has a Pt/HfO x /n-type indium-gallium-zinc oxide (n-IGZO) structure. The three-terminal synaptic TFT exhibits a tunable synaptic weight with a drain current modulation upon repeated application of gate and drain voltages. The synaptic weight modulation is analog, voltage-polarity dependent reversible, and strong with a dynamic range of multiple orders of magnitude (>10 4 ). This modulation process emulates biological synaptic potentiation, depression, excitatory-postsynaptic current, paired-pulse facilitation, and short-term to long-term memory transition behaviors as a result of repeated pulsing with respect to the pulse amplitude, width, repetition number, and the interval between pulses. These synaptic behaviors are interpreted based on the changes in the capacitance of the Pt/HfO x /n-IGZO gate stack, the channel mobility, and the threshold voltage that result from the redistribution of oxygen ions by the applied gate voltage. These results demonstrate the potential of this structure for three-terminal synaptic transistor using the gate stack composed of the HfO x gate insulator and the IGZO channel layer.

Synaptic behaviors of thin-film transistor with a Pt/HfO x /n-type indium–gallium–zinc oxide gate stack

NASA Astrophysics Data System (ADS)

Yang, Paul; Park, Daehoon; Beom, Keonwon; Kim, Hyung Jun; Kang, Chi Jung; Yoon, Tae-Sik

2018-07-01

We report a variety of synaptic behaviors in a thin-film transistor (TFT) with a metal-oxide-semiconductor gate stack that has a Pt/HfO x /n-type indium–gallium–zinc oxide (n-IGZO) structure. The three-terminal synaptic TFT exhibits a tunable synaptic weight with a drain current modulation upon repeated application of gate and drain voltages. The synaptic weight modulation is analog, voltage-polarity dependent reversible, and strong with a dynamic range of multiple orders of magnitude (>104). This modulation process emulates biological synaptic potentiation, depression, excitatory-postsynaptic current, paired-pulse facilitation, and short-term to long-term memory transition behaviors as a result of repeated pulsing with respect to the pulse amplitude, width, repetition number, and the interval between pulses. These synaptic behaviors are interpreted based on the changes in the capacitance of the Pt/HfO x /n-IGZO gate stack, the channel mobility, and the threshold voltage that result from the redistribution of oxygen ions by the applied gate voltage. These results demonstrate the potential of this structure for three-terminal synaptic transistor using the gate stack composed of the HfO x gate insulator and the IGZO channel layer.

Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches.

PubMed

Jain, Niyati; Zhao, Liang; Liu, John D; Xia, Tianbing

2010-05-04

High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding and base stacking interactions, yielding the high affinity and specificity by the aptamer domain.

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Wideband analytical equivalent circuit for one-dimensional periodic stacked arrays.

PubMed

Molero, Carlos; Rodríguez-Berral, Raúl; Mesa, Francisco; Medina, Francisco; Yakovlev, Alexander B

2016-01-01

A wideband equivalent circuit is proposed for the accurate analysis of scattering from a set of stacked slit gratings illuminated by a plane wave with transverse magnetic or electric polarization that impinges normally or obliquely along one of the principal planes of the structure. The slit gratings are printed on dielectric slabs of arbitrary thickness, including the case of closely spaced gratings that interact by higher-order modes. A Π-circuit topology is obtained for a pair of coupled arrays, with fully analytical expressions for all the circuit elements. This equivalent Π circuit is employed as the basis to derive the equivalent circuit of finite stacks with any given number of gratings. Analytical expressions for the Brillouin diagram and the Bloch impedance are also obtained for infinite periodic stacks.

Discrete breathers dynamic in a model for DNA chain with a finite stacking enthalpy

NASA Astrophysics Data System (ADS)

Gninzanlong, Carlos Lawrence; Ndjomatchoua, Frank Thomas; Tchawoua, Clément

2018-04-01

The nonlinear dynamics of a homogeneous DNA chain based on site-dependent finite stacking and pairing enthalpies is studied. A new variant of extended discrete nonlinear Schrödinger equation describing the dynamics of modulated wave is derived. The regions of discrete modulational instability of plane carrier waves are studied, and it appears that these zones depend strongly on the phonon frequency of Fourier's mode. The staggered/unstaggered discrete breather (SDB/USDB) is obtained straightforwardly without the staggering transformation, and it is demonstrated that SDBs are less unstable than USDB. The instability of discrete multi-humped SDB/USDB solution does not depend on the number of peaks of the discrete breather (DB). By using the concept of Peierls-Nabarro energy barrier, it appears that the low-frequency DBs are more mobile.

Direct Observation of Excimer-Mediated Intramolecular Electron Transfer in a Cofacially-Stacked Perylene Bisimide Pair.

PubMed

Sung, Jooyoung; Nowak-Król, Agnieszka; Schlosser, Felix; Fimmel, Benjamin; Kim, Woojae; Kim, Dongho; Würthner, Frank

2016-07-27

We have elucidated excimer-mediated intramolecular electron transfer in cofacially stacked PBIs tethered by two phenylene-butadiynylene loops. The electron transfer between energetically equivalent PBIs is revealed by the simultaneous observation of the PBI radical anion and cation bands in the transient absorption spectra. The fluorescence decay time of the excimer states is in good agreement with the rise time of PBI radical bands in transient absorption spectra suggesting that the electron transfer dynamics proceed via the excimer state. We can conclude that the excimer state effectuates the efficient charge transfer in the cofacially stacked PBI dimer.

Cell separator for use in bipolar-stack energy storage devices

DOEpatents

Mayer, Steven T.; Feikert, John H.; Kachmitter, James L.; Pekala, Richard W.

1995-01-01

An improved multi-cell electrochemical energy storage device, such as a battery, fuel cell, or double layer capacitor using a cell separator which allows cells to be stacked and interconnected with low electrical resistance and high reliability while maximizing packaging efficiency. By adding repeating cells, higher voltages can be obtained. The cell separator is formed by applying an organic adhesive on opposing surfaces of adjacent carbon electrodes or surfaces of aerogel electrodes of a pair of adjacent cells prior to or after pyrolysis thereof to form carbon aerogel electrodes. The cell separator is electronically conductive, but ionically isolating, preventing an electrolytic conduction path between adjacent cells in the stack.

Layout designs of surface barrier coatings for boosting the capability of oxygen/vapor obstruction utilized in flexible electronics

NASA Astrophysics Data System (ADS)

Lee, Chang-Chun; Huang, Pei-Chen; He, Jing-Yan

2018-04-01

Organic light-emitting diode-based flexible and rollable displays have become a promising candidate for next-generation flexible electronics. For this reason, the design of surface multi-layered barriers should be optimized to enhance the long-term mechanical reliability of a flexible encapsulation that prevents the penetration of oxygen and vapor. In this study, finite element-based stress simulation was proposed to estimate the mechanical reliability of gas/vapor barrier design with low-k/silicon nitride (low-k/SiNx) stacking architecture. Consequently, stress-induced failure of critical thin films within the flexible display under various bending conditions must be considered. The feasibility of one pair SiO2/SiNx barrier design, which overcomes the complex lamination process, and the critical bending radius, which is decreased to 1.22 mm, were also examined. In addition, the influence of distance between neutral axes to the concerned layer surface dominated the induced-stress magnitude rather than the stress compliant mechanism provided from stacked low-k films.

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

Yankee Tank Creek Observatory Report No. 1: Forty-One Measures from 2012

NASA Astrophysics Data System (ADS)

Wiley, E. O.

2014-01-01

This report contains 41 measures of mostly STF pairs taken in 2012 and comprises those pairs not reported in other papers. All measures were taken with a 0.2M Dall-Kirkham and a DMK21 video camera working at F22.5. Both stacking and pixel correlation techniques were used to obtain measures using REDUC.

Recognition of T·G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies

PubMed Central

Lacy, Eilyn R.; Cox, Kari K.; Wilson, W. David; Lee, Moses

2002-01-01

An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize T·G mismatched base pairs. In order to characterize in detail the T·G recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson–Crick and mismatched (containing one or two T·G, A·G or G·G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the T·G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson–Crick base pairs. Compared with the Watson–Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing T·G mismatches in place of one or two C·G base pairs and, more importantly, the dissociation rate from the T·G oligonucleotides is very slow (small kd). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower kd values with the T·G mismatched duplexes. CD titration studies of f-ImImIm complexes with T·G mismatched sequences produce strong induced bands at ∼330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation. PMID:11937638

The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

PubMed

Bende, Attila; Muntean, Cristina M

2014-03-01

The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

X-ray and neutron total scattering analysis of Hy·(Bi0.2Ca0.55Sr0.25)(Ag0.25Na0.75)Nb3O10·xH2O perovskite nanosheet booklets with stacking disorder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metz, Peter; Koch, Robert; Cladek, Bernadette

Ion-exchanged Aurivillius materials form perovskite nanosheet booklets wherein well-defined bi-periodic sheets, with ~11.5 Å thickness, exhibit extensive stacking disorder. The perovskite layer contents were defined initially using combined synchrotron X-ray and neutron Rietveld refinement of the parent Aurivillius structure. The structure of the subsequently ion-exchanged material, which is disordered in its stacking sequence, is analyzed using both pair distribution function (PDF) analysis and recursive method simulations of the scattered intensity. Combined X-ray and neutron PDF refinement of supercell stacking models demonstrates sensitivity of the PDF to both perpendicular and transverse stacking vector components. Further, hierarchical ensembles of stacking models weightedmore » by a standard normal distribution are demonstrated to improve PDF fit over 1–25 Å. Recursive method simulations of the X-ray scattering profile demonstrate agreement between the real space stacking analysis and more conventional reciprocal space methods. The local structure of the perovskite sheet is demonstrated to relax only slightly from the Aurivillius structure after ion exchange.« less

Compliance Testing of Eielson Air Force Base Central Heating and Power Plant, Coal Fired Boiler Number 3, Eielson Air Force Base, Alaska

DTIC Science & Technology

1988-12-01

a flue gas grab sample for orsat analysis (measures oxygen, and carbon dioxide for stack gas molecular weight determination and emissions correction... molecular weight, was obtained during particulate sampling. Testing was initially started on boiler 2 at the maximum rated steam output of 120,000 lbs/hr...I, r*~td AN[D l FL B( R\\ ViQ( lPjN L!II(,t 1 (d) Open burning of put.rcible iear- i\\ % ~i~ emisions , ec.dirig c dn jc p. c ,f1 pre- cri :rig pair

Expansion of the Genetic Alphabet: A Chemist's Approach to Synthetic Biology.

PubMed

Feldman, Aaron W; Romesberg, Floyd E

2018-02-20

The information available to any organism is encoded in a four nucleotide, two base pair genetic code. Since its earliest days, the field of synthetic biology has endeavored to impart organisms with novel attributes and functions, and perhaps the most fundamental approach to this goal is the creation of a fifth and sixth nucleotide that pair to form a third, unnatural base pair (UBP) and thus allow for the storage and retrieval of increased information. Achieving this goal, by definition, requires synthetic chemistry to create unnatural nucleotides and a medicinal chemistry-like approach to guide their optimization. With this perspective, almost 20 years ago we began designing unnatural nucleotides with the ultimate goal of developing UBPs that function in vivo, and thus serve as the foundation of semi-synthetic organisms (SSOs) capable of storing and retrieving increased information. From the beginning, our efforts focused on the development of nucleotides that bear predominantly hydrophobic nucleobases and thus that pair not based on the complementary hydrogen bonds that are so prominent among the natural base pairs but rather via hydrophobic and packing interactions. It was envisioned that such a pairing mechanism would provide a basal level of selectivity against pairing with natural nucleotides, which we expected would be the greatest challenge; however, this choice mandated starting with analogs that have little or no homology to their natural counterparts and that, perhaps not surprisingly, performed poorly. Progress toward their optimization was driven by the construction of structure-activity relationships, initially from in vitro steady-state kinetic analysis, then later from pre-steady-state and PCR-based assays, and ultimately from performance in vivo, with the results augmented three times with screens that explored combinations of the unnatural nucleotides that were too numerous to fully characterize individually. The structure-activity relationship data identified multiple features required by the UBP, and perhaps most prominent among them was a substituent ortho to the glycosidic linkage that is capable of both hydrophobic packing and hydrogen bonding, and nucleobases that stably stack with flanking natural nucleobases in lieu of the potentially more stabilizing stacking interactions afforded by cross strand intercalation. Most importantly, after the examination of hundreds of unnatural nucleotides and thousands of candidate UBPs, the efforts ultimately resulted in the identification of a family of UBPs that are well recognized by DNA polymerases when incorporated into DNA and that have been used to create SSOs that store and retrieve increased information. In addition to achieving a longstanding goal of synthetic biology, the results have important implications for our understanding of both the molecules and forces that can underlie biological processes, so long considered the purview of molecules benefiting from eons of evolution, and highlight the promise of applying the approaches and methodologies of synthetic and medical chemistry in the pursuit of synthetic biology.

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting.

PubMed

Cornish, Peter V; Hennig, Mirko; Giedroc, David P

2005-09-06

The molecular determinants of stimulation of -1 programmed ribosomal frameshifting (-1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes -1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3' nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2'-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2'-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of -1 PRF (15 +/- 2%) relative to the BWYV pseudoknot (6 +/- 1%), a difference traced largely to the identity of the 3' nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by approximately 1.5 kcal x mol(-1) (pH 7.0, 37 degrees C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated –1 ribosomal frameshifting

PubMed Central

Cornish, Peter V.; Hennig, Mirko; Giedroc, David P.

2005-01-01

The molecular determinants of stimulation of –1 programmed ribosomal frameshifting (–1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes –1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3′ nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2′-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1–2′-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2–S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of –1 PRF (15 ± 2%) relative to the BWYV pseudoknot (6 ± 1%), a difference traced largely to the identity of the 3′ nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by ≈1.5 kcal·mol–1 (pH 7.0, 37°C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs. PMID:16123125

Method for forming a cell separator for use in bipolar-stack energy storage devices

DOEpatents

Mayer, Steven T.; Feikert, John H.; Kaschmitter, James L.; Pekala, Richard W.

1994-01-01

An improved multi-cell electrochemical energy storage device, such as a battery, fuel cell, or double layer capacitor using a cell separator which allows cells to be stacked and interconnected with low electrical resistance and high reliability while maximizing packaging efficiency. By adding repeating cells, higher voltages can be obtained. The cell separator is formed by applying an organic adhesive on opposing surfaces of adjacent carbon electrodes or surfaces of aerogel electrodes of a pair of adjacent cells prior to or after pyrolysis thereof to form carbon aerogel electrodes. The cell separator is electronically conductive, but ionically isolating, preventing an electrolytic conduction path between adjacent cells in the stack.

Cell separator for use in bipolar-stack energy storage devices

DOEpatents

Mayer, S.T.; Feikert, J.H.; Kachmitter, J.L.; Pekala, R.W.

1995-02-28

An improved multi-cell electrochemical energy storage device is described, such as a battery, fuel cell, or double layer capacitor using a cell separator which allows cells to be stacked and interconnected with low electrical resistance and high reliability while maximizing packaging efficiency. By adding repeating cells, higher voltages can be obtained. The cell separator is formed by applying an organic adhesive on opposing surfaces of adjacent carbon electrodes or surfaces of aerogel electrodes of a pair of adjacent cells prior to or after pyrolysis thereof to form carbon aerogel electrodes. The cell separator is electronically conductive, but ionically isolating, preventing an electrolytic conduction path between adjacent cells in the stack. 2 figs.

Method for forming a cell separator for use in bipolar-stack energy storage devices

DOEpatents

Mayer, S.T.; Feikert, J.H.; Kaschmitter, J.L.; Pekala, R.W.

1994-08-09

An improved multi-cell electrochemical energy storage device, such as a battery, fuel cell, or double layer capacitor using a cell separator which allows cells to be stacked and interconnected with low electrical resistance and high reliability while maximizing packaging efficiency. By adding repeating cells, higher voltages can be obtained. The cell separator is formed by applying an organic adhesive on opposing surfaces of adjacent carbon electrodes or surfaces of aerogel electrodes of a pair of adjacent cells prior to or after pyrolysis thereof to form carbon aerogel electrodes. The cell separator is electronically conductive, but ionically isolating, preventing an electrolytic conduction path between adjacent cells in the stack. 2 figs.

Polyarene mediators for mediated redox flow battery

DOEpatents

Delnick, Frank M.; Ingersoll, David; Liang, Chengdu

2018-01-02

The fundamental charge storage mechanisms in a number of currently studied high energy redox couples are based on intercalation, conversion, or displacement reactions. With exception to certain metal-air chemistries, most often the active redox materials are stored physically in the electrochemical cell stack thereby lowering the practical gravimetric and volumetric energy density as a tradeoff to achieve reasonable power density. In a general embodiment, a mediated redox flow battery includes a series of secondary organic molecules that form highly reduced anionic radicals as reaction mediator pairs for the reduction and oxidation of primary high capacity redox species ex situ from the electrochemical cell stack. Arenes are reduced to stable anionic radicals that in turn reduce a primary anode to the charged state. The primary anode is then discharged using a second lower potential (more positive) arene. Compatible separators and solvents are also disclosed herein.

Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing

PubMed Central

Lebars, Isabelle; Lamontagne, Bruno; Yoshizawa, Satoko; Abou Elela, Sherif; Fourmy, Dominique

2001-01-01

Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A–A or A–C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5′ side of the loop, exposing their Watson–Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage. PMID:11743001

Characterization of stacked-crystal PET detector designs for measurement of both TOF and DOI.

PubMed

Schmall, Jeffrey P; Surti, Suleman; Karp, Joel S

2015-05-07

A PET detector with good timing resolution and two-level depth-of-interaction (DOI) discrimination can be constructed using a single-ended readout of scintillator stacks of Lanthanum Bromide (LaBr3), with various Cerium dopant concentrations, including pure Cerium Bromide (CeBr3). The stacked crystal geometry creates a unique signal shape for interactions occurring in each layer, which can be used to identify the DOI, while retaining the inherently good timing properties of LaBr3 and CeBr3. In this work, single pixel elements are used to optimize the choice of scintillator, coupling of layers, and type of photodetector, evaluating the performance using a fast, single-channel photomultiplier tube (PMT) and a single 4 × 4 mm(2) silicon photomultiplier (SiPM). We also introduce a method to quantify and evaluate the DOI discrimination accuracy. From signal shape measurements using fast waveform sampling, we found that in addition to differences in signal rise times, between crystal layers, there were also differences in the signal fall times. A DOI accuracy of 98% was achieved using our classification method for a stacked crystal pair, consisting of a 15 mm long LaBr3(Ce:20%) crystal on top of a 15 mm long CeBr3 crystal, readout using a PMT. A DOI accuracy of 95% was measured with a stack of two, identical, 12 mm long, CeBr3 crystals. The DOI accuracy of this crystal pair was reduced to 91% when using a SiPM for readout. For the stack of two, 12 mm long, CeBr3 crystals, a coincidence timing resolution (average of timing results from the top and bottom layer) of 199 ps was measured using a PMT, and this was improved to 153 ps when using a SiPM. These results show that with stacked LaBr3/CeBr3 scintillators and fast waveform sampling nearly perfect DOI accuracy can be achieved with excellent timing resolution-timing resolution that is only minimally degraded compared to results from a single CeBr3 crystal of comparable length to the stacked crystals. The interface in the stacked crystal geometry itself plays a major role in creating the differences in signal shape and this can be used to construct stacked DOI detectors using the same scintillator type, thereby simplifying and broadening the application of this technique.

Characterization of stacked-crystal PET detector designs for measurement of both TOF and DOI

PubMed Central

Schmall, Jeffrey P; Surti, Suleman; Karp, Joel S

2015-01-01

A PET detector with good timing resolution and two-level depth-of-interaction (DOI) discrimination can be constructed using a single-ended readout of scintillator stacks of Lanthanum Bromide (LaBr3), with various Cerium dopant concentrations, including pure Cerium Bromide (CeBr3). The stacked crystal geometry creates a unique signal shape for interactions occurring in each layer, which can be used to identify the DOI, while retaining the inherently good timing properties of LaBr3 and CeBr3. In this work, single pixel elements are used to optimize the choice of scintillator, coupling of layers, and type of photodetector, evaluating the performance using a fast, single-channel photomultiplier tube (PMT) and a single 4×4 mm2 silicon photomultiplier (SiPM). We also introduce a method to quantify and evaluate the DOI discrimination accuracy. From signal shape measurements using fast waveform sampling, we found that in addition to differences in signal rise times, between crystal layers, there were also differences in the signal fall times. A DOI accuracy of 98% was achieved using our classification method for a stacked crystal pair, consisting of a 15-mm long LaBr3(Ce:20%) crystal on top of a 15-mm long CeBr3 crystal, readout using a PMT. A DOI accuracy of 95% was measured with a stack of two, identical, 12-mm long, CeBr3 crystals. The DOI accuracy of this crystal pair was reduced to 91% when using a SiPM for readout. For the stack of two, 12-mm long, CeBr3 crystals, a coincidence timing resolution (average of timing results from the top and bottom layer) of 199 ps was measured using a PMT, and this was improved to 153 ps when using a SiPM. These results show that with stacked LaBr3/CeBr3 scintillators and fast waveform sampling nearly perfect DOI accuracy can be achieved with excellent timing resolution—timing resolution that is only minimally degraded compared to results from a single CeBr3 crystal of comparable length to the stacked crystals. The interface in the stacked crystal geometry itself plays a major role in creating the differences in signal shape and this can be used to construct stacked DOI detectors using the same scintillator type, thereby simplifying and broadening the application of this technique. PMID:25860172

Fragment charge difference method for estimating donor-acceptor electronic coupling: Application to DNA π-stacks

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.; Rösch, Notker

2002-09-01

The purpose of this communication is two-fold. We introduce the fragment charge difference (FCD) method to estimate the electron transfer matrix element HDA between a donor D and an acceptor A, and we apply this method to several aspects of hole transfer electronic couplings in π-stacks of DNA, including systems with several donor-acceptor sites. Within the two-state model, our scheme can be simplified to recover a convenient estimate of the electron transfer matrix element HDA=(1-Δq2)1/2(E2-E1)/2 based on the vertical excitation energy E2-E1 and the charge difference Δq between donor and acceptor. For systems with strong charge separation, Δq≳0.95, one should resort to the FCD method. As favorable feature, we demonstrate the stability of the FCD approach for systems which require an approach beyond the two-state model. On the basis of ab initio calculations of various DNA related systems, we compared three approaches for estimating the electronic coupling: the minimum splitting method, the generalized Mulliken-Hush (GMH) scheme, and the FCD approach. We studied the sensitivity of FCD and GMH couplings to the donor-acceptor energy gap and found both schemes to be quite robust; they are applicable also in cases where donor and acceptor states are off resonance. In the application to π-stacks of DNA, we demonstrated for the Watson-Crick pair dimer [(GC),(GC)] how structural changes considerably affect the coupling strength of electron hole transfer. For models of three Watson-Crick pairs, we showed that the two-state model significantly overestimates the hole transfer coupling whereas simultaneous treatment of several states leads to satisfactory results.

The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine.

PubMed Central

Lynch, S R; Tinoco, I

1998-01-01

The structure of the L3 central hairpin loop isolated from the antigenomic sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems from the ribozyme stacked on top of the loop has been determined by NMR spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a 7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient catalysis in the intact ribozyme. The structure was determined using homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled RNA oligonucleotides. The overall root mean square deviation for the structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but without the lone purine in the loop, which is not well defined in the structure. The structure indicates a U.C base pair between the nucleotides on the 5'- and 3'-ends of the loop. This base pair is formed with a single hydrogen bond involving the cytosine exocyclic amino proton and the carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn cytidine. While not unprecedented, syn pyrimidines are highly unusual. This one can be confidently established by intranucleotide distances between the ribose and the base determined by NMR spectroscopy. A similar study of the structure of this loop showed a somewhat different three-dimensional structure. A discussion of differences in the two structures, as well as possible sites of interaction with the cleavage site, will be presented. PMID:9461457

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

PubMed Central

Pack, Seung Pil; Morimoto, Hirohisa; Makino, Keisuke; Tajima, Kunihiko; Kanaori, Kenji

2012-01-01

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases. PMID:22039100

Zebra finch mates use their forebrain song system in unlearned call communication.

PubMed

Ter Maat, Andries; Trost, Lisa; Sagunsky, Hannes; Seltmann, Susanne; Gahr, Manfred

2014-01-01

Unlearned calls are produced by all birds whereas learned songs are only found in three avian taxa, most notably in songbirds. The neural basis for song learning and production is formed by interconnected song nuclei: the song control system. In addition to song, zebra finches produce large numbers of soft, unlearned calls, among which "stack" calls are uttered frequently. To determine unequivocally the calls produced by each member of a group, we mounted miniature wireless microphones on each zebra finch. We find that group living paired males and females communicate using bilateral stack calling. To investigate the role of the song control system in call-based male female communication, we recorded the electrical activity in a premotor nucleus of the song control system in freely behaving male birds. The unique combination of acoustic monitoring together with wireless brain recording of individual zebra finches in groups shows that the neuronal activity of the song system correlates with the production of unlearned stack calls. The results suggest that the song system evolved from a brain circuit controlling simple unlearned calls to a system capable of producing acoustically rich, learned vocalizations.

Ultra-thin distributed Bragg reflectors via stacked single-crystal silicon nanomembranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Minkyu; Seo, Jung-Hun; Lee, Jaeseong

2015-05-04

In this paper, we report ultra-thin distributed Bragg reflectors (DBRs) via stacked single-crystal silicon (Si) nanomembranes (NMs). Mesh hole-free single-crystal Si NMs were released from a Si-on-insulator substrate and transferred to quartz and Si substrates. Thermal oxidation was applied to the transferred Si NM to form high-quality SiO{sub 2} and thus a Si/SiO{sub 2} pair with uniform and precisely controlled thicknesses. The Si/SiO{sub 2} layers, as smooth as epitaxial grown layers, minimize scattering loss at the interface and in between the layers. As a result, a reflection of 99.8% at the wavelength range from 1350 nm to 1650 nm can be measuredmore » from a 2.5-pair DBR on a quartz substrate and 3-pair DBR on a Si substrate with thickness of 0.87 μm and 1.14 μm, respectively. The high reflection, ultra-thin DBRs developed here, which can be applied to almost any devices and materials, holds potential for application in high performance optoelectronic devices and photonics applications.« less

Dovetail spoke internal permanent magnet machine

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-08-23

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a stator magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple pair of permanent magnets for generating a magnetic field, which magnetic field interacts with the stator magnetic field to produce a torque. The multiple pair of permanent magnets are disposed between the stacks. The rotor assembly also includes multiple middle wedges mounted between each pair of the multiple permanent magnets.

Effect of stacking faults on the magnetocrystalline anisotropy of hcp Co: a first-principles study.

PubMed

Aas, C J; Szunyogh, L; Evans, R F L; Chantrell, R W

2013-07-24

In terms of the fully relativistic screened Korringa-Kohn-Rostoker method we investigate the effect of stacking faults on the magnetic properties of hexagonal close-packed (hcp) cobalt. In particular, we consider the formation energy and the effect on the magnetocrystalline anisotropy energy (MAE) of four different stacking faults in hcp cobalt-an intrinsic growth fault, an intrinsic deformation fault, an extrinsic fault and a twin-like fault. We find that the intrinsic growth fault has the lowest formation energy, in good agreement with previous first-principles calculations. With the exception of the intrinsic deformation fault which has a positive impact on the MAE, we find that the presence of a stacking fault generally reduces the MAE of bulk Co. Finally, we consider a pair of intrinsic growth faults and find that their effect on the MAE is not additive, but synergic.

Crustal Imaging of the Faroe Islands and North Sea Using Ambient Seismic Noise

NASA Astrophysics Data System (ADS)

Sammarco, C.; Rawlinson, N.; Cornwell, D. G.

2016-12-01

The recent development of ambient seismic noise imaging offers the potential for obtaining detailed seismic models of the crust. Cross-correlation of long-term recordings from station pairs reveals an empirical "Green's function" which is related to the impulse response of the medium between the two stations. Here, we present new results using two different broadband datasets: one that spans the Faroe Islands and another that spans the North Sea. The smaller scale Faroe Islands study was tackled first, because with only 12 stations, it was well suited for the development and testing of a new data processing and inversion workflow. In the Faroe Islands study cross-correlations with high signal-to-noise ratios were obtained by applying phase weighted stacking, which is shown to be a significant improvement over convectional linear stacking. For example, coherent noise concentrated near the zero time lag of the linearly stacked cross correlations appears to have an influence on the dispersion characteristics beyond 10 s period, but we have managed to minimize these effects with phase weighted stacking. We obtain group velocity maps from 0.5s to 15s period by inverting inter-station travel times using an iterative non-linear inversion scheme. It reveals the presence of significant lateral heterogeneity in the mid-upper crust, including evidence of a low velocity zone in the upper crust, which may mark the base of the basalt layer. This is most clearly revealed by taking the average group velocity dispersion curve for all station pairs and inverting for 1-D shear wave velocity. The computation of a 3-D shear wave speed model both verifies and adds further detail to these results. Application to the North Sea dataset was challenging due to the highly attenuative nature of the crust in this region, which has previously been observed to dramatically reduce the signal-to-noise ratio of short period surface waves. However, with the help of phase-weighted stacking good quality empirical Green's functions can be retrieved for this large dataset. Both group and phase velocity dispersion information are extracted from the cross-correlations, which are then inverted to produce period-dependent velocity maps. The next stage is to invert these maps for 3-D shear wave velocity structure beneath the North Sea region.

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

PubMed Central

Chen, Chin-Yu; Ko, Tzu-Ping; Lin, Ting-Wan; Chou, Chia-Cheng; Chen, Chun-Jung; Wang, Andrew H.-J.

2005-01-01

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (∼60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant–DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (∼50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (∼80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower Tm values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA. PMID:15653643

Derivatization of DNAs with Selenium at 6-Position of Guanine for Function and Crystal Structure Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salon, J.; Jiang, J; Sheng, J

2008-01-01

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm ({Epsilon} = 2.3 x 10{sup 4} M{sup -1} cm{sup -1}), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination andmore » analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se H-N), and the {sup Se}G and C form a base pair similar to the natural G-C pair though the Se-modification causes the base-pair to shift (approximately 0.3 {angstrom}). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.« less

DNA dynamics in aqueous solution: opening the double helix

NASA Technical Reports Server (NTRS)

Pohorille, A.; Ross, W. S.; Tinoco, I. Jr; MacElroy, R. D. (Principal Investigator)

1990-01-01

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

Method and apparatus for adding electrolyte to a fuel cell stack

DOE Office of Scientific and Technical Information (OSTI.GOV)

Congdon, J.V.; English, J.G.

1986-06-24

A process is described for adding electrolyte to a fuel cell stack, the stack comprising sheet-like elements defining a plurality of fuel cell units disposed one atop the other in abutting relationship, the units defining a substantially flat, vertically extending face, each unit including a cell comprising a pair of sheet-like spaced apart gas porous electrodes with a porous matrix layer sandwiched therebetween for retaining electrolyte during cell operation, each unit also including a sheet-like substantially non-porous separator, the separator being sandwiched between the cells of adjacent units. The improvement described here consists of: extending at least one of themore » sheet-like elements of each of a plurality of the fuel cell units outwardly from the stack face to define horizontal tabs disposed one above the other; depositing dilute electrolyte directly from electrolyte supply means upon substantially the full length, parallel to the stack face, of at least the uppermost tab, the tabs being constructed and arranged such that at least a portion of the deposited electrolyte cascades from tab to tab and down the face of the stack, the deposited electrolyte being absorbed by capillary action into the elements of the stack, the step of depositing continuing until all of the electrodes and matrix layers of the stack are fully saturated with the dilute electrolyte; and thereafter evaporating liquid from the saturated elements under controlled conditions of humidity and temperature until the stack has a desired electrolyte volume and electrolyte concentration therein.« less

Breath stacking in children with neuromuscular disorders.

PubMed

Jenkins, H M; Stocki, A; Kriellaars, D; Pasterkamp, H

2014-06-01

Respiratory muscle weakness in neuromuscular disorders (NMD) can lead to shallow breathing and respiratory insufficiency over time. Children with NMD often cannot perform maneuvers to recruit lung volume. In adults, breath stacking with a mask and one-way valve can achieve significantly increased lung volumes. To evaluate involuntary breath stacking (IBS) in NMD, we studied 23 children of whom 15 were cognitively aware and able to communicate verbally. For IBS, a one-way valve and pneumotachograph were attached to a face mask. Tidal volumes (Vt) and minute ventilation (VE ) were calculated from airflow over 30 sec before and after 15 sec of expiratory valve closure. Six cooperative male subjects with Duchenne muscular dystrophy (DMD) participated in a subsequent comparison of IBS with voluntary breath stacking (VBS) and supported breath stacking (SBS). The average Vt in those studied with IBS was 277 ml (range 29-598 ml). The average increase in volume by stacking was 599 ml (range -140 to 2,916 ml) above Vt . The average number of stacked breaths was 4.5 (range 0-17). VE increased on average by 18% after stacking (P < 0.05, paired t-test). Oxygen saturation did not change after stacking. Four of the 23 children did not breath stack. Compared to IBS, VBS achieved similar volumes in the six subjects with DMD but SBS was more successful in those with greatest muscle weakness. IBS may achieve breath volumes of approximately three times Vt and may be particularly useful in non-cooperative subjects with milder degrees of respiratory muscle weakness. © 2013 Wiley Periodicals, Inc.

Base pairing and structural insights into the 5-formylcytosine in RNA duplex

PubMed Central

Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

2016-01-01

Abstract 5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

Electrolyte chemistry control in electrodialysis processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayes, Thomas D.; Severin, Blaine F.

Methods for controlling electrolyte chemistry in electrodialysis units having an anode and a cathode each in an electrolyte of a selected concentration and a membrane stack disposed therebetween. The membrane stack includes pairs of cationic selective and anionic membranes to segregate increasingly dilute salts streams from concentrated salts stream. Electrolyte chemistry control is via use of at least one of following techniques: a single calcium exclusionary cationic selective membrane at a cathode cell boundary, an exclusionary membrane configured as a hydraulically isolated scavenger cell, a multivalent scavenger co-electrolyte and combinations thereof.

Space Radiation Detector with Spherical Geometry

NASA Technical Reports Server (NTRS)

Wrbanek, John D. (Inventor); Fralick, Gustave C. (Inventor); Wrbanek, Susan Y. (Inventor)

2011-01-01

A particle detector is provided, the particle detector including a spherical Cherenkov detector, and at least one pair of detector stacks. In an embodiment of the invention, the Cherenkov detector includes a sphere of ultraviolet transparent material, coated by an ultraviolet reflecting material that has at least one open port. The Cherenkov detector further includes at least one photodetector configured to detect ultraviolet light emitted from a particle within the sphere. In an embodiment of the invention, each detector stack includes one or more detectors configured to detect a particle traversing the sphere.

Space Radiation Detector with Spherical Geometry

NASA Technical Reports Server (NTRS)

Wrbanek, John D. (Inventor); Fralick, Gustave C. (Inventor); Wrbanek, Susan Y. (Inventor)

2012-01-01

A particle detector is provided, the particle detector including a spherical Cherenkov detector, and at least one pair of detector stacks. In an embodiment of the invention, the Cherenkov detector includes a sphere of ultraviolet transparent material, coated by an ultraviolet reflecting material that has at least one open port. The Cherenkov detector further includes at least one photodetector configured to detect ultraviolet light emitted from a particle within the sphere. In an embodiment of the invention, each detector stack includes one or more detectors configured to detect a particle traversing the sphere.

Base Flipping in V(D)J Recombination: Insights into the Mechanism of Hairpin Formation, the 12/23 Rule, and the Coordination of Double-Strand Breaks▿ †

PubMed Central

Bischerour, Julien; Lu, Catherine; Roth, David B.; Chalmers, Ronald

2009-01-01

Tn5 transposase cleaves the transposon end using a hairpin intermediate on the transposon end. This involves a flipped base that is stacked against a tryptophan residue in the protein. However, many other members of the cut-and-paste transposase family, including the RAG1 protein, produce a hairpin on the flanking DNA. We have investigated the reversed polarity of the reaction for RAG recombination. Although the RAG proteins appear to employ a base-flipping mechanism using aromatic residues, the putatively flipped base is not at the expected location and does not appear to stack against any of the said aromatic residues. We propose an alternative model in which a flipped base is accommodated in a nonspecific pocket or cleft within the recombinase. This is consistent with the location of the flipped base at position −1 in the coding flank, which can be occupied by purine or pyrimidine bases that would be difficult to stabilize using a single, highly specific, interaction. Finally, during this work we noticed that the putative base-flipping events on either side of the 12/23 recombination signal sequence paired complex are coupled to the nicking steps and serve to coordinate the double-strand breaks on either side of the complex. PMID:19720743

An integration machine for the assembly of the x-ray optic units based on thin slumped glass foils for the IXO mission

NASA Astrophysics Data System (ADS)

Civitani, M. M.; Basso, S.; Bavdaz, M.; Citterio, O.; Conconi, P.; Gallieni, D.; Ghigo, M.; Martelli, F.; Pareschi, G.; Parodi, G.; Proserpio, L.; Sironi, G.; Spiga, D.; Tagliaferri, G.; Tintori, M.; Wille, E.; Zambra, A.

2011-09-01

The International X-ray Observatory (IXO) is a joint mission concept studied by the ESA, NASA, and JAXA space agencies. The main goal of the mission design is to achieve a large effective area (>2.5m2 at 1 keV) and a good angular resolution (5 arcsec HEW at 1 keV) at the same time. The Brera Astronomical Observatory - INAF, Italy), under the support of ESA, is developing a method for the realization of the X-Ray Optical Units, based on the use of slumped thin glass segments to form densely packed modules in a Wolter type I optical configuration. In order to reach the very challenging integration requirements, it has been developed an innovative assembly approach for aligning and mounting the IXO mirror segments. The method is based on the use of an integration mould for each foil. In particular the glass segment is forced to adhere to the integration mould in order to maintain the optimal figure without deformations until the integration of the foil in the stack is completed. In this way an active correction for major existing figure errors after slumping is also achieved. Moreover reinforcing ribs are used in order to connect the facets to each-other and to realize a robust monolithic stack of plates. In this paper we present the design, the development and the validation status of a special Integration Machine (IMA) that has been specifically developed to allow the integration of the Plate Pairs into prototypal X-Ray Optical Unit stacks.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

PubMed

Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

2013-12-01

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. Copyright © 2013 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

An intercalation-locked parallel-stranded DNA tetraplex

DOE PAGES

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

2015-01-27

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

Strain-Driven Stacking Faults in CdSe/CdS Core/Shell Nanorods.

PubMed

Demortière, Arnaud; Leonard, Donovan N; Petkov, Valeri; Chapman, Karena; Chattopadhyay, Soma; She, Chunxing; Cullen, David A; Shibata, Tomohiro; Pelton, Matthew; Shevchenko, Elena V

2018-04-19

Colloidal semiconductor nanocrystals are commonly grown with a shell of a second semiconductor material to obtain desired physical properties, such as increased photoluminescence quantum yield. However, the growth of a lattice-mismatched shell results in strain within the nanocrystal, and this strain has the potential to produce crystalline defects. Here, we study CdSe/CdS core/shell nanorods as a model system to investigate the influence of core size and shape on the formation of stacking faults in the nanocrystal. Using a combination of high-angle annular dark-field scanning transmission electron microscopy and pair-distribution-function analysis of synchrotron X-ray scattering, we show that growth of the CdS shell on smaller, spherical CdSe cores results in relatively small strain and few stacking faults. By contrast, growth of the shell on larger, prolate spheroidal cores leads to significant strain in the CdS lattice, resulting in a high density of stacking faults.

Serrated kiln sticks and top load substantially reduce warp in southern pine studs dried at 240°F

Treesearch

Peter Koch

1974-01-01

Sharply toothed aluminum kiln sticks pressed into 2 by 4's cut from veneer cores, with a clamping force of 50 to 200 pounds per stick-pair per stud, significantly reduced warp from that observed in matched studs stacked on smooth sticks with a top load of 10 pounds per stick-pair per stud. When dried in 24 hours to an average MC of 8.1 percent (standard deviation...

Serrated kiln sticks and top load substantially reduce warp in southern pine studs dried at 240°F

Treesearch

P. Koch

1974-01-01

Sharply toothed luminum kiln sticks pressed into 2 by 4's cut from veneer cores, willi a clamping force of 50 to 200 pounds per stick-pair per stud, significantly reduced warp from that observed in matched studs stacked on smooth sticks with a top load of 10 pounds per stick-pair per stud. When dried in 24 hours to an average MC of 8.1 percent (standard deviation...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venkadesh, S.; Mandal, P.K.; Gautham, N., E-mail: n_gautham@hotmail.com

Highlights: {yields} This is the first crystal structure of a four-way junction with sticky ends. {yields} Four junction structures bind to each other and form a rhombic cavity. {yields} Each rhombus binds to others to form 'infinite' 2D tiles. {yields} This is an example of bottom-up fabrication of a DNA nano-lattice. -- Abstract: We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind tomore » each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5 A. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.« less

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

The impact of base stacking on the conformations and electrostatics of single-stranded DNA.

PubMed

Plumridge, Alex; Meisburger, Steve P; Andresen, Kurt; Pollack, Lois

2017-04-20

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Quencher-Free Fluorescence Method for the Detection of Mercury(II) Based on Polymerase-Aided Photoinduced Electron Transfer Strategy.

PubMed

Liu, Haisheng; Ma, Linbin; Ma, Changbei; Du, Junyan; Wang, Meilan; Wang, Kemin

2016-11-18

A new quencher-free Hg 2+ ion assay method was developed based on polymerase-assisted photoinduced electron transfer (PIET). In this approach, a probe is designed with a mercury ion recognition sequence (MRS) that is composed of two T-rich functional areas separated by a spacer of random bases at the 3'-end, and a sequence of stacked cytosines at the 5'-end, to which a fluorescein (FAM) is attached. Upon addition of Hg 2+ ions into this sensing system, the MRS folds into a hairpin structure at the 3'-end with Hg 2+ -mediated base pairs. In the presence of DNA polymerase, it will catalyze the extension reaction, resulting in the formation of stacked guanines, which will instantly quench the fluorescence of FAM through PIET. Under optimal conditions, the limit of detection for Hg 2+ ions was estimated to be 5 nM which is higher than the US Environmental Protection Agency (EPA) standard limit. In addition, no labeling with a quencher was requiring, and the present method is fairly simple, fast and low cost. It is expected that this cost-effective fluorescence method might hold considerable potential in the detection of Hg 2+ ions in real biological and environmental samples.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

Structure-affinity relationships for the binding of actinomycin D to DNA

NASA Astrophysics Data System (ADS)

Gallego, José; Ortiz, Angel R.; de Pascual-Teresa, Beatriz; Gago, Federico

1997-03-01

Molecular models of the complexes between actinomycin D and 14 different DNA hexamers were built based on the X-ray crystal structure of the actinomycin-d(GAAGCTTC)2 complex. The DNA sequences included the canonical GpC binding step flanked by different base pairs, nonclassical binding sites such as GpG and GpT, and sites containing 2,6-diamino- purine. A good correlation was found between the intermolecular interaction energies calculated for the refined complexes and the relative preferences of actinomycin binding to standard and modified DNA. A detailed energy decomposition into van der Waals and electrostatic components for the interactions between the DNA base pairs and either the chromophore or the peptidic part of the antibiotic was performed for each complex. The resulting energy matrix was then subjected to principal component analysis, which showed that actinomycin D discriminates among different DNA sequences by an interplay of hydrogen bonding and stacking interactions. The structure-affinity relationships for this important antitumor drug are thus rationalized and may be used to advantage in the design of novel sequence-specific DNA-binding agents.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

Guanine base stacking in G-quadruplex nucleic acids

PubMed Central

Lech, Christopher Jacques; Heddi, Brahim; Phan, Anh Tuân

2013-01-01

G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another within the G-tetrad core. Individual G-quadruplexes can also stack with one another at their G-tetrad interface leading to higher-order structures as observed in telomeric repeat-containing DNA and RNA. In this study, we investigate how guanine base stacking influences the stability of G-quadruplexes and their stacked higher-order structures. A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. We couple this survey with a systematic computational examination of stacked G-tetrad energy landscapes using quantum mechanical computations. Energy calculations of stacked G-tetrads reveal large energy differences of up to 12 kcal/mol between experimentally observed geometries at the interface of stacked G-quadruplexes. Energy landscapes are also computed using an AMBER molecular mechanics description of stacking energy and are shown to agree quite well with quantum mechanical calculated landscapes. Molecular dynamics simulations provide a structural explanation for the experimentally observed preference of parallel G-quadruplexes to stack in a 5′–5′ manner based on different accessible tetrad stacking modes at the stacking interfaces of 5′–5′ and 3′–3′ stacked G-quadruplexes. PMID:23268444

Proposal of a Bulk HTSC Staggered Array Undulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kii, Toshiteru; Kinjo, Ryota; Bakr, Mahmoud A.

We proposed a new type of undulator based on bulk high-T{sub c} superconductors (HTSC) which consists of a single solenoid and a stacked array of bulk HTSC. The main advantage of this configuration is that a mechanical structure is not required to produce and control the undulator field. In order to perform a proof of principle experiment, we have developed a prototype of bulk HTSC staggered array undulator using 11 pairs of DyBaCuO bulk superconductors and a normal conducting solenoid. Experimental results obtained by using the prototype undulator and numerical results obtained by a loop current model based on themore » Bean mode for a type-II superconductor were compared.« less

Photoactive devices including porphyrinoids with coordinating additives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K

Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths,more » increase the external quantum efficiency of the material, or both.« less

Electrically tunable g factors in quantum dot molecular spin states.

PubMed

Doty, M F; Scheibner, M; Ponomarev, I V; Stinaff, E A; Bracker, A S; Korenev, V L; Reinecke, T L; Gammon, D

2006-11-10

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Electrically Tunable g Factors in Quantum Dot Molecular Spin States

NASA Astrophysics Data System (ADS)

Doty, M. F.; Scheibner, M.; Ponomarev, I. V.; Stinaff, E. A.; Bracker, A. S.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

2006-11-01

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Three-dimensional negative index of refraction at optical frequencies by coupling plasmonic waveguides.

PubMed

Verhagen, Ewold; de Waele, René; Kuipers, L; Polman, Albert

2010-11-26

We identify a route towards achieving a negative index of refraction at optical frequencies based on coupling between plasmonic waveguides that support backwards waves. We show how modal symmetry can be exploited in metal-dielectric waveguide pairs to achieve negative refraction of both phase and energy. Control of waveguide coupling yields a metamaterial consisting of a one-dimensional multilayer stack that exhibits an isotropic index of -1 at a free-space wavelength of 400 nm. The concepts developed here may inspire new low-loss metamaterial designs operating close to the metal plasma frequency.

Extracting surface waves, hum and normal modes: time-scale phase-weighted stack and beyond

NASA Astrophysics Data System (ADS)

Ventosa, Sergi; Schimmel, Martin; Stutzmann, Eleonore

2017-10-01

Stacks of ambient noise correlations are routinely used to extract empirical Green's functions (EGFs) between station pairs. The time-frequency phase-weighted stack (tf-PWS) is a physically intuitive nonlinear denoising method that uses the phase coherence to improve EGF convergence when the performance of conventional linear averaging methods is not sufficient. The high computational cost of a continuous approach to the time-frequency transformation is currently a main limitation in ambient noise studies. We introduce the time-scale phase-weighted stack (ts-PWS) as an alternative extension of the phase-weighted stack that uses complex frames of wavelets to build a time-frequency representation that is much more efficient and fast to compute and that preserve the performance and flexibility of the tf-PWS. In addition, we propose two strategies: the unbiased phase coherence and the two-stage ts-PWS methods to further improve noise attenuation, quality of the extracted signals and convergence speed. We demonstrate that these approaches enable to extract minor- and major-arc Rayleigh waves (up to the sixth Rayleigh wave train) from many years of data from the GEOSCOPE global network. Finally we also show that fundamental spheroidal modes can be extracted from these EGF.

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Imaging Subsurface Structure of Central Zagros Zone/Iran Using Ambient Noise Tomography

NASA Astrophysics Data System (ADS)

Vahidravesh, Shaghayegh; Pakzad, Mehrdad, ,, Dr.; Hatami, Mohammad Reza, ,, Dr.

2017-04-01

The Central Zagros zone, of west Iran & east Iraq, is surrounded by many active faults (including Main Zagros Reversed Fault, Main Recent Fault, High Zagros Fault, Zagros Fold, & Thrust Belt). Recent studies show that cross-correlation of a long-term ambient seismic noise data recorded in station-pair, includes important information regarding empirical Green's functions (EGFs) between stations. Hence, ambient seismic noise carries valuable information of the wave propagation path (which can be extracted). The 2D model of surface waves (Rayleigh & Love) velocities for the studied area is obtained by seismic ambient noise tomography (ANT) method. Throughout this research, we use continuous records of all three vertical, radial, and tangential components (obtained by rotation) recorded by IRSC (Iranian Seismological Center) and IIEES (International Institute of Earthquake Engineering) networks for this area of interest. The IRSC & IIEES networks are equipped by SS-1 kinematics and Guralp CMG-3T sensors respectively. Data of 20 stations were used for 12 months from 2014/Nov. to 2015/Nov. The performed data processing is similar to the one, put into words in detail by Bensen et al. (2007) including the processed daily base data. Mean, trend, and instrument response were removed and the data were decimated to 5 sps (sample per second) to reduce the amount of storage space and computational time required. We then applied merge to handle data gaps. One-bit time-domain normalization was also applied to suppress the influence of instrument irregularities and earthquake signals followed by spectral (frequency-domain) normalization between 0.05-0.2 Hz (period 5-20 sec). After cross-correlation (processing step), we perform rms stacking (new approach of stacking) to stack many cross-correlation functions based on the highest energy in a time interval which we accordingly anticipate to receive Rayleigh & Love waves fundamental modes. To evaluate quality of the stacking process stability quantitatively, we calculate signal-to-noise ratio (SNR), defined as a ratio of the peak amplitude within a time window to the root-mean-square of noise trailing the signal arrival window (Bensen et al., 2007), for each cross-correlation. The cross-correlated time-series is equivalent to the Green's functions between pairs of receivers. We then apply multiple phase-matched filter method of Herrmann (2005) to measure the correct group velocity dispersion of the interferometric surface waves. Eventually, we apply fast marching surface wave tomography (FMST), the iterative nonlinear inversion package developed by Rawlinson, 2005, to extract the velocity model of shallow structure in Central Zagros zone /Iran.

Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

PubMed

Efimov, Alexander V; Spirin, Alexander S

2009-10-09

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

ZN graded discrete Lax pairs and Yang-Baxter maps

NASA Astrophysics Data System (ADS)

Fordy, Allan P.; Xenitidis, Pavlos

2017-05-01

We recently introduced a class of ZN graded discrete Lax pairs and studied the associated discrete integrable systems (lattice equations). In this paper, we introduce the corresponding Yang-Baxter maps. Many well-known examples belong to this scheme for N=2, so, for N≥3, our systems may be regarded as generalizations of these. In particular, for each N we introduce a class of multi-component Yang-Baxter maps, which include H^{B_{III (of Papageorgiou et al. 2010 SIGMA 6, 003 (9 p). (doi:10.3842/SIGMA.2010.033)), when N=2, and that associated with the discrete modified Boussinesq equation, for N=3. For N≥5 we introduce a new family of Yang-Baxter maps, which have no lower dimensional analogue. We also present new multi-component versions of the Yang-Baxter maps FIV and FV (given in the classification of Adler et al. 2004 Commun. Anal. Geom. 12, 967-1007. (doi:10.4310/CAG.2004.v12.n5.a1)).}}

Long-Lived Correlated Triplet Pairs in a π-Stacked Crystalline Pentacene Derivative.

PubMed

Folie, Brendan D; Haber, Jonah B; Refaely-Abramson, Sivan; Neaton, Jeffrey B; Ginsberg, Naomi S

2018-02-14

Singlet fission is the spin-conserving process by which a singlet exciton splits into two triplet excitons. Singlet fission occurs via a correlated triplet pair intermediate, but direct evidence of this state has been scant, and in films of TIPS-pentacene, a small molecule organic semiconductor, even the rate of fission has been unclear. We use polarization-resolved transient absorption microscopy on individual crystalline domains of TIPS-pentacene to establish the fission rate and demonstrate that the initially created triplets remain bound for a surprisingly long time, hundreds of picoseconds, before separating. Furthermore, using a broadband probe, we show that it is possible to determine absorbance spectra of individual excited species in a crystalline solid. We find that triplet interactions perturb the absorbance, and provide evidence that triplet interaction and binding could be caused by the π-stacked geometry. Elucidating the relationship between the lattice structure and the electronic structure and dynamics has important implications for the creation of photovoltaic devices that aim to boost efficiency via singlet fission.

Comparison of Interferometric Time-Series Analysis Techniques with Implications for Future Mission Design

NASA Astrophysics Data System (ADS)

Werner, C. L.; Wegmuller, U.; Strozzi, T.; Wiesmann, A.

2006-12-01

Principle contributors to the noise in differential SAR interferograms are temporal phase stability of the surface, geometry relating to baseline and surface slope, and propagation path delay variations due to tropospheric water vapor and the ionosphere. Time series analysis of multiple interferograms generated from a stack of SAR SLC images seeks to determine the deformation history of the surface while reducing errors. Only those scatterers within a resolution element that are stable and coherent for each interferometric pair contribute to the desired deformation signal. Interferograms with baselines exceeding 1/3 the critical baseline have substantial geometrical decorrelation for distributed targets. Short baseline pairs with multiple reference scenes can be combined using least-squares estimation to obtain a global deformation solution. Alternately point-like persistent scatterers can be identified in scenes that do not exhibit geometrical decorrelation associated with large baselines. In this approach interferograms are formed from a stack of SAR complex images using a single reference scene. Stable distributed scatter pixels are excluded however due to the presence of large baselines. We apply both point- based and short-baseline methodologies and compare results for a stack of fine-beam Radarsat data acquired in 2002-2004 over a rapidly subsiding oil field near Lost Hills, CA. We also investigate the density of point-like scatters with respect to image resolution. The primary difficulty encountered when applying time series methods is phase unwrapping errors due to spatial and temporal gaps. Phase unwrapping requires sufficient spatial and temporal sampling. Increasing the SAR range bandwidth increases the range resolution as well as increasing the critical interferometric baseline that defines the required satellite orbital tube diameter. Sufficient spatial sampling also permits unwrapping because of the reduced phase/pixel gradient. Short time intervals further reduce the differential phase due to deformation when the deformation is continuous. Lower frequency systems (L- vs. C-Band) substantially improve the ability to unwrap the phase correctly by directly reducing both interferometric phase amplitude and temporal decorrelation.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

NASA Astrophysics Data System (ADS)

Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

2015-06-01

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.

2015-06-21

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including thosemore » corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.« less

DNA Electrochemistry with Tethered Methylene Blue

PubMed Central

Pheeney, Catrina G.

2012-01-01

Methylene blue (MB′), covalently attached to DNA through a flexible C12 alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB′ is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 ± 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB′–DNA is found to be least 3-fold larger than that of Nile blue (NB)–DNA, indicating that MB′ is even more strongly coupled to the π-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB′ on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions. PMID:22512327

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

PubMed

Bandyopadhyay, Dibyendu; Bhanja, K; Mohan, Sadhana; Ghosh, Swapan K; Choudhury, Niharendu

2015-08-27

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs.

PubMed

Marchetti, Barbara; Karsili, Tolga N V; Ashfold, Michael N R; Domcke, Wolfgang

2016-07-27

The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.

Thermal stability of DNA quadruplex-duplex hybrids.

PubMed

Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

2014-01-14

DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

Low hydrostatic head electrolyte addition to fuel cell stacks

DOEpatents

Kothmann, Richard E.

1983-01-01

A fuel cell and system for supply electrolyte, as well as fuel and an oxidant to a fuel cell stack having at least two fuel cells, each of the cells having a pair of spaced electrodes and a matrix sandwiched therebetween, fuel and oxidant paths associated with a bipolar plate separating each pair of adjacent fuel cells and an electrolyte fill path for adding electrolyte to the cells and wetting said matrices. Electrolyte is flowed through the fuel cell stack in a back and forth fashion in a path in each cell substantially parallel to one face of opposite faces of the bipolar plate exposed to one of the electrodes and the matrices to produce an overall head uniformly between cells due to frictional pressure drop in the path for each cell free of a large hydrostatic head to thereby avoid flooding of the electrodes. The bipolar plate is provided with channels forming paths for the flow of the fuel and oxidant on opposite faces thereof, and the fuel and the oxidant are flowed along a first side of the bipolar plate and a second side of the bipolar plate through channels formed into the opposite faces of the bipolar plate, the fuel flowing through channels formed into one of the opposite faces and the oxidant flowing through channels formed into the other of the opposite faces.

Galaxy and Mass Assembly (GAMA): probing the merger histories of massive galaxies via stellar populations

NASA Astrophysics Data System (ADS)

Ferreras, I.; Hopkins, A. M.; Gunawardhana, M. L. P.; Sansom, A. E.; Owers, M. S.; Driver, S.; Davies, L.; Robotham, A.; Taylor, E. N.; Konstantopoulos, I.; Brough, S.; Norberg, P.; Croom, S.; Loveday, J.; Wang, L.; Bremer, M.

2017-06-01

The merging history of galaxies can be traced with studies of dynamically close pairs. These consist of a massive primary galaxy and a less massive secondary (or satellite) galaxy. The study of the stellar populations of secondary (lower mass) galaxies in close pairs provides a way to understand galaxy growth by mergers. Here we focus on systems involving at least one massive galaxy - with stellar mass above 1011M⊙ in the highly complete Galaxy and Mass Assembly (GAMA) survey. Our working sample comprises 2692 satellite galaxy spectra (0.1 ≤ z ≤ 0.3). These spectra are combined into high S/N stacks, and binned according to both an 'internal' parameter, the stellar mass of the satellite galaxy (I.e. the secondary), and an 'external' parameter, selecting either the mass of the primary in the pair, or the mass of the corresponding dark matter halo. We find significant variations in the age of the populations with respect to environment. At fixed mass, satellites around the most massive galaxies are older and possibly more metal-rich, with age differences ˜1-2 Gyr within the subset of lower mass satellites (˜1010 M⊙). These variations are similar when stacking with respect to the halo mass of the group where the pair is embedded. The population trends in the lower mass satellites are consistent with the old stellar ages found in the outer regions of massive galaxies.

Test results of 12/18 kA ReBCO coated conductor current leads

NASA Astrophysics Data System (ADS)

Kovalev, I. A.; Surin, M. I.; Naumov, A. V.; Novikov, M. S.; Novikov, S. I.; Ilin, A. A.; Polyakov, A. V.; Scherbakov, V. I.; Shutova, D. I.

2017-07-01

A pair of hybrid current leads (brass + stacked & soldered ReBCO tapes) rated for 12 kA in steady state and for up to 18 kA at pulsed over current conditions was designed, developed and tested at NRC ;Kurchatov Institute; (NRC ;KI;). During the experiment at LN2 temperature, the current leads (CLs) were successfully charged with 18 kA at 100 A/s ramp rate. To date, as far as we know, this is the highest current capacity achieved for 2G HTS current leads. The feasibility of ;stack-and-soldering technique; for 10 kA+ class coated conductor CLs for accelerators and fusion was demonstrated. This paper gives an overview of the leads design and presents the preliminary test results. Detailed studies of magnetic properties and current sharing process for the stacked and staggered HTS joints are also reported.

A twice-paired watershed experimental design to assess stacked practices through field-edge monitoring

USDA-ARS?s Scientific Manuscript database

To improve our ability to reduce nutrient losses from agricultural lands to receiving waters, comprehensive approaches that employ a variety of conservation practices placed within and below field edges will be needed. There is a need to obtain experimental data to better understand how conservation...

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

PubMed

Sedova, Ada; Banavali, Nilesh K

2017-03-14

Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

An asymmetric mesoscopic model for single bulges in RNA

NASA Astrophysics Data System (ADS)

de Oliveira Martins, Erik; Weber, Gerald

2017-10-01

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Live-cell imaging of dual-labeled Golgi stacks in tobacco BY-2 cells reveals similar behaviors for different cisternae during movement and brefeldin A treatment.

PubMed

Madison, Stephanie L; Nebenführ, Andreas

2011-09-01

In plant cells, the Golgi apparatus consists of numerous stacks that, in turn, are composed of several flattened cisternae with a clear cis-to-trans polarity. During normal functioning within living cells, this unusual organelle displays a wide range of dynamic behaviors such as whole stack motility, constant membrane flux through the cisternae, and Golgi enzyme recycling through the ER. In order to further investigate various aspects of Golgi stack dynamics and integrity, we co-expressed pairs of established Golgi markers in tobacco BY-2 cells to distinguish sub-compartments of the Golgi during monensin treatments, movement, and brefeldin A (BFA)-induced disassembly. A combination of cis and trans markers revealed that Golgi stacks remain intact as they move through the cytoplasm. The Golgi stack orientation during these movements showed a slight preference for the cis side moving ahead, but trans cisternae were also found at the leading edge. During BFA treatments, the different sub-compartments of about half of the observed stacks fused with the ER sequentially; however, no consistent order could be detected. In contrast, the ionophore monensin resulted in swelling of trans cisternae while medial and particularly cis cisternae were mostly unaffected. Our results thus demonstrate a remarkable equivalence of the different cisternae with respect to movement and BFA-induced fusion with the ER. In addition, we propose that a combination of dual-label fluorescence microscopy and drug treatments can provide a simple alternative approach to the determination of protein localization to specific Golgi sub-compartments.

Observing Holliday junction branch migration one step at a time

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2004-03-01

During genetic recombination, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction and the recognition and processing of this species by branch migration and junction resolving enzymes determine the outcome. We have used single molecule fluorescence techniques to study two intrinsic structural dynamics of the Holliday junction, stacking conformer transitions and spontaneous branch migration. Our studies show that the dynamics of branch migration, resolved with one base pair resolution, is determined by the stability of conformers which in turn depends on the local DNA sequences. Therefore, the energy landscape of Holliday junction branch migation is not uniform, but is rugged.

Microelectromechanical mirrors and electrically-programmable diffraction gratings based on two-stage actuation

DOEpatents

Allen, James J.; Sinclair, Michael B.; Dohner, Jeffrey L.

2005-11-22

A microelectromechanical (MEM) device for redirecting incident light is disclosed. The MEM device utilizes a pair of electrostatic actuators formed one above the other from different stacked and interconnected layers of polysilicon to move or tilt an overlying light-reflective plate (i.e. a mirror) to provide a reflected component of the incident light which can be shifted in phase or propagation angle. The MEM device, which utilizes leveraged bending to provide a relatively-large vertical displacement up to several microns for the light-reflective plate, has applications for forming an electrically-programmable diffraction grating (i.e. a polychromator) or a micromirror array.

The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain*S⃞♦

PubMed Central

Spitale, Robert C.; Torelli, Andrew T.; Krucinska, Jolanta; Bandarian, Vahe; Wedekind, Joseph E.

2009-01-01

Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ1 riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ1 aptamer domain in complex with its precursor metabolite preQ0. The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated. PMID:19261617

Fluorometric graphene oxide-based detection of Salmonella enteritis using a truncated DNA aptamer.

PubMed

Chinnappan, Raja; AlAmer, Saleh; Eissa, Shimaa; Rahamn, Anas Abdel; Abu Salah, Khalid M; Zourob, Mohammed

2017-12-18

The work describes a fluorescence-based study for mapping the highest affinity truncated aptamer from the full length sequence and its integration in a graphene oxide platform for the detection of Salmonella enteriditis. To identify the best truncated sequence, molecular beacons and a displacement assay design are applied. In the fluorescence displacement assay, the truncated aptamer was hybridized with fluorescein and quencher-labeled complementary sequences to form a fluorescence/quencher pair. In the presence of S. enteritidis, the aptamer dissociates from the complementary labeled oligonucleotides and thus, the fluorescein/quencher pair becomes physically separated. This leads to an increase in fluorescence intensity. One of the truncated aptamers identified has a 2-fold lower dissociation constant (3.2 nM) compared to its full length aptamer (6.3 nM). The truncated aptamer selected in this process was used to develop a fluorometric graphene oxide (GO) based assay. If fluorescein-labeled aptamer is adsorbed on GO via π stacking interaction, fluorescence is quenched. However, in the presence of target (S. enteriditis), the labeled aptamers is released from surface to form a stable complex with the bacteria and fluorescence is restored, depending on the quantity of bacteria being present. The resulting assay has an unsurpassed detection limit of 25 cfu·mL -1 in the best case. The cross reactivity to Salmonella typhimurium, Staphylococcus aureus and Escherichia coli is negligible. The assay was applied to analyze doped milk samples for and gave good recovery. Thus, we believe that the truncated aptamer/graphene oxide platform is a potential tool for the detection of S. Enteritidis. Graphical abstract Fluorescently labelled aptamer against Salmonella enteritidis was adsorbed on the surface of graphene oxide by π-stacking interaction. This results in quenching of the fluorescence of the label. Addition of Salmonella enteritidis restores fluorescence, and this effect is used for quantification of this food-borne pathogen.

Method for Making a Fuel Cell from a Solid Oxide Monolithic Framework

NASA Technical Reports Server (NTRS)

Sofie, Stephen W. (Inventor); Cable, Thomas L. (Inventor)

2014-01-01

The invention is a novel solid oxide fuel cell (SOFC) stack comprising individual bi-electrode supported fuel cells in which a thin electrolyte is supported between electrodes of essentially equal thickness. Individual cell units are made from graded pore ceramic tape that has been created by the freeze cast method followed by freeze drying. Each piece of graded pore tape later becomes a graded pore electrode scaffold that subsequent to sintering, is made into either an anode or a cathode by means of appropriate solution and thermal treatment means. Each cell unit is assembled by depositing of a thin coating of ion conducting ceramic material upon the side of each of two pieces of tape surface having the smallest pore openings, and then mating the coated surfaces to create an unsintered electrode scaffold pair sandwiching an electrolyte layer. The opposing major outer exposed surfaces of each cell unit is given a thin coating of electrically conductive ceramic, and multiple cell units are stacked, or built up by stacking of individual cell layers, to create an unsintered fuel cell stack. Ceramic or glass edge seals are installed to create flow channels for fuel and air. The cell stack with edge sealants is then sintered into a ceramic monolithic framework. Said solution and thermal treatments means convert the electrode scaffolds into anodes and cathodes. The thin layers of electrically conductive ceramic become the interconnects in the assembled stack.

Performance Testing of Tracer Gas and Tracer Aerosol Detectors for use in Radionuclide NESHAP Compliance Testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuehne, David Patrick; Lattin, Rebecca Renee

The Rad-NESHAP program, part of the Air Quality Compliance team of LANL’s Compliance Programs group (EPC-CP), and the Radiation Instrumentation & Calibration team, part of the Radiation Protection Services group (RP-SVS), frequently partner on issues relating to characterizing air flow streams. This memo documents the most recent example of this partnership, involving performance testing of sulfur hexafluoride detectors for use in stack gas mixing tests. Additionally, members of the Rad-NESHAP program performed a functional trending test on a pair of optical particle counters, comparing results from a non-calibrated instrument to a calibrated instrument. Prior to commissioning a new stack samplingmore » system, the ANSI Standard for stack sampling requires that the stack sample location must meet several criteria, including uniformity of tracer gas and aerosol mixing in the air stream. For these mix tests, tracer media (sulfur hexafluoride gas or liquid oil aerosol particles) are injected into the stack air stream and the resulting air concentrations are measured across the plane of the stack at the proposed sampling location. The coefficient of variation of these media concentrations must be under 20% when evaluated over the central 2/3 area of the stack or duct. The instruments which measure these air concentrations must be tested prior to the stack tests in order to ensure their linear response to varying air concentrations of either tracer gas or tracer aerosol. The instruments used in tracer gas and aerosol mix testing cannot be calibrated by the LANL Standards and Calibration Laboratory, so they would normally be sent off-site for factory calibration by the vendor. Operational requirements can prevent formal factory calibration of some instruments after they have been used in hazardous settings, e.g., within a radiological facility with potential airborne contamination. The performance tests described in this document are intended to demonstrate the reliable performance of the test instruments for the specific tests used in stack flow characterization.« less

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

PubMed

Spasic, Aleksandar; Kennedy, Scott D; Needham, Laura; Manoharan, Muthiah; Kierzek, Ryszard; Turner, Douglas H; Mathews, David H

2018-05-01

The RNA "GAGU" duplex, (5'GAC GAGU GUCA) 2 , contains the internal loop (5'-GAGU-3') 2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans -Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'- endo conformation. This differs markedly from the internal loops, (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-UAGG-3') 2 , which all have cis -Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis -Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-U AG G-3') 2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3') 2 , equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3') 2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3') 2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed. © 2018 Spasic et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Mirror mount

DOEpatents

Kuklo, Thomas C.; Bender, Donald A.

1994-01-01

A unique lens or mirror mount having adjustable constraints at two key locations to allow for "X" and "Y" tilts of the mirror only. The device uses two pair of flexures of a type such that the pivots of the mirror gimble are rigidly fixed in all planes allowing the device to have zero stacking tolerance and zero wear over time.

Woven-grid sealed quasi-bipolar lead-acid battery construction and fabricating method

NASA Technical Reports Server (NTRS)

Rippel, Wally E. (Inventor)

1989-01-01

A quasi-bipolar lead-acid battery construction includes a plurality of bipolar cells disposed in side-by-side relation to form a stack, and a pair of monoplanar plates at opposite ends of the stack, the cell stack and monopolar plates being contained within a housing of the battery. Each bipolar cell is loaded with an electrolyte and composed of a bipolar electrode plate and a pair of separator plates disposed on opposite sides of the electrode plate and peripherally sealed thereto. Each bipolar electrode plate is composed of a partition sheet and two bipolar electrode elements folded into a hairpin configuration and applied over opposite edges of the partition sheet so as to cover the opposite surfaces of the opposite halves thereof. Each bipolar electrode element is comprised of a woven grid with a hot-melt strip applied to a central longitudinal region of the grid along which the grid is folded into the hairpin configuration, and layers of negative and positive active material pastes applied to opposite halves of the grid on opposite sides of the central hot-melt strip. The grid is made up of strands of conductive and non-conductive yarns composing the respective transverse and longitudinal weaves of the grid. The conductive yarn has a multi-stranded glass core surrounded and covered by a lead sheath, whereas the non-conductive yarn has a multi-stranded glass core surrounded and covered by a thermally activated sizing.

Sequence-Dependent Elasticity and Electrostatics of Single-Stranded DNA: Signatures of Base-Stacking

PubMed Central

McIntosh, Dustin B.; Duggan, Gina; Gouil, Quentin; Saleh, Omar A.

2014-01-01

Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer’s rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼−0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration. PMID:24507606

How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation.

PubMed

Wu, Wen-Jin; Su, Mei-I; Wu, Jian-Li; Kumar, Sandeep; Lim, Liang-Hin; Wang, Chun-Wei Eric; Nelissen, Frank H T; Chen, Ming-Chuan Chad; Doreleijers, Jurgen F; Wijmenga, Sybren S; Tsai, Ming-Daw

2014-04-02

A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix αE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.

Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study.

PubMed

Miyahara, Tomoo; Nakatsuji, Hiroshi; Sugiyama, Hiroshi

2016-11-17

The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data.

PubMed

Pitonák, Michal; Neogrády, Pavel; Cerný, Jirí; Grimme, Stefan; Hobza, Pavel

2009-01-12

Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.

A Novel Method of Building Functional Brain Network Using Deep Learning Algorithm with Application in Proficiency Detection.

PubMed

Hua, Chengcheng; Wang, Hong; Wang, Hong; Lu, Shaowen; Liu, Chong; Khalid, Syed Madiha

2018-04-11

Functional brain network (FBN) has become very popular to analyze the interaction between cortical regions in the last decade. But researchers always spend a long time to search the best way to compute FBN for their specific studies. The purpose of this study is to detect the proficiency of operators during their mineral grinding process controlling based on FBN. To save the search time, a novel semi-data-driven method of computing functional brain connection based on stacked autoencoder (BCSAE) is proposed in this paper. This method uses stacked autoencoder (SAE) to encode the multi-channel EEG data into codes and then computes the dissimilarity between the codes from every pair of electrodes to build FBN. The highlight of this method is that the SAE has a multi-layered structure and is semi-supervised, which means it can dig deeper information and generate better features. Then an experiment was performed, the EEG of the operators were collected while they were operating and analyzed to detect their proficiency. The results show that the BCSAE method generated more number of separable features with less redundancy, and the average accuracy of classification (96.18%) is higher than that of the control methods: PLV (92.19%) and PLI (78.39%).

Preliminary Seismic Velocity Structure Results from Ambient Noise and Teleseismic Tomography: Laguna del Maule Volcanic Field, Chile

NASA Astrophysics Data System (ADS)

Wespestad, C.; Thurber, C. H.; Zeng, X.; Bennington, N. L.; Cardona, C.; Singer, B. S.

2016-12-01

Laguna del Maule Volcanic Field is a large, restless, rhyolitic system in the Southern Andes that is being heavily studied through several methods, including seismology, by a collaborative team of research institutions. A temporary array of 52 seismometers from OVDAS (the Southern Andean Volcano Observatory), PASSCAL (Portable Array Seismic Studies of the Continental Lithosphere), and the University of Wisconsin-Madison was used to collect the 1.3 years worth of data for this preliminary study. Ambient noise tomography uses surface wave dispersion data obtained from noise correlation functions (NCFs) between pairs of seismic stations, with one of each pair acting as a virtual source, in order to image the velocity structure in 3-D. NCFs were computed for hour-long time windows, and the final NCFs were obtained with phase-weighted stacking. The Frequency-Time Analysis technique was then utilized to measure group velocity between station pairs. NCFs were also analyzed to detect temporal changes in seismic velocity related to magmatic activity at the volcano. With the surface wave data from ambient noise, our small array aperture limits our modeling to the upper crust, so we employed teleseismic tomography to study deeper structures. For picking teleseismic arrivals, we tested two different correlation and stacking programs, which utilize adaptive stacking and multi-channel cross-correlation, to get relative arrival time data for a set of high quality events. Selected earthquakes were larger than magnitude 5 and between 30 and 95 degrees away from the center of the array. Stations that consistently show late arrivals may have a low velocity body beneath them, more clearly visualized via a 3-D tomographic model. Initial results from the two tomography methods indicate the presence of low-velocity zones at several depths. Better resolved velocity models will be developed as more data are acquired.

Nanoscale heterogeneity as remnant hexagonal-type local structures in shocked Cu-Pb and Zr

NASA Astrophysics Data System (ADS)

Tayal, Akhil; Conradson, Steven D.; Batuk, Olga N.; Fensin, Saryu; Cerreta, Ellen; Gray, George T.; Saxena, Avadh

2017-09-01

Extended X-ray absorption fine structure spectroscopy was used to determine the local structure in: (1) Zr that had undergone quasistatic elongation; (2) Zr that had undergone plastic deformation by shock at pressures above and below the ω-phase transformation; and (3) shocked Cu that contained a few percent of insoluble Pb. Below the transition pressure, Zr samples showed only general disorder as increases in the widths of the Zr-Zr pair distributions. Above this pressure, Zr that was a mixture of the original hcp and the high pressure ω-phase when measured by diffraction showed two sets of peaks in its distribution corresponding to these two phases. Some of the ones from the ω-phase were at distances substantially different from those calculated from the diffraction pattern, although they are still consistent with small domains exhibiting stacking faults associated with hexagonal-type structural components exhibiting variability in the [0001] basal plane spacing. A similar result, new pairs at just over 3 and 4 Å consistent with hexagonal-type stacking faults in addition to the original fcc structure, is found in shocked Cu despite the absence of a second diffraction pattern and peak pressures being far below those expected to induce an fcc to hcp transition. This result, therefore, demonstrates that the correlation between high strain rates and reduced stacking fault energy continues down to the length scale of atom pairs. These findings are significant as: (1) a microscopic description of the behavior of systems far from equilibrium; (2) a demonstration of the importance of strain rate at short length scales; and (3) a bridge between the abruptness of macroscopic pressure-induced phase transitions and the continuity of martensitic ones over their fluctuation region in terms of the inverse relationship between the length scale of the martensitic texture, manifested here as ordered lattice distortions and the lower pressure at which such texture first appears relative to the bulk transition pressure.

5-Nitro-N 4,N 6-diphenyl­pyrimidine-4,6-diamine: polarized mol­ecules linked into π-stacked chains via three-centre C—H⋯(O)2 hydrogen bonds

PubMed Central

Rodríguez, Ricaurte; Nogueras, Manuel; Cobo, Justo; Glidewell, Christopher

2009-01-01

Mol­ecules of the title compound, C16H13N5O2, have no inter­nal symmetry despite the symmetric pattern of substitution in the pyrimidine ring. The intra­molecular distances indicate polarization of the electronic structure. There are two intra­molecular N—H⋯O hydrogen bonds and mol­ecules are linked into centrosymmetric dimers by pairs of three-centre C—H⋯(O)2 hydrogen bonds. These dimers are linked into chains by means of a π–π stacking inter­action. PMID:19726856

AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide.

PubMed

Satam, Vijay; Babu, Balaji; Patil, Pravin; Brien, Kimberly A; Olson, Kevin; Savagian, Mia; Lee, Megan; Mepham, Andrew; Jobe, Laura Beth; Bingham, John P; Pett, Luke; Wang, Shuo; Ferrara, Maddi; Bruce, Chrystal D; Wilson, W David; Lee, Moses; Hartley, John A; Kiakos, Konstantinos

2015-09-01

The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)). Copyright © 2015 Elsevier Ltd. All rights reserved.

Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA

PubMed Central

Cristóvão, Michele; Sisamakis, Evangelos; Hingorani, Manju M.; Marx, Andreas D.; Jung, Caroline P.; Rothwell, Paul J.; Seidel, Claus A. M.; Friedhoff, Peter

2012-01-01

Mismatch repair (MMR) corrects replication errors such as mismatched bases and loops in DNA. The evolutionarily conserved dimeric MMR protein MutS recognizes mismatches by stacking a phenylalanine of one subunit against one base of the mismatched pair. In all crystal structures of G:T mismatch-bound MutS, phenylalanine is stacked against thymine. To explore whether these structures reflect directional mismatch recognition by MutS, we monitored the orientation of Escherichia coli MutS binding to mismatches by FRET and anisotropy with steady state, pre-steady state and single-molecule multiparameter fluorescence measurements in a solution. The results confirm that specifically bound MutS bends DNA at the mismatch. We found additional MutS–mismatch complexes with distinct conformations that may have functional relevance in MMR. The analysis of individual binding events reveal significant bias in MutS orientation on asymmetric mismatches (G:T versus T:G, A:C versus C:A), but not on symmetric mismatches (G:G). When MutS is blocked from binding a mismatch in the preferred orientation by positioning asymmetric mismatches near the ends of linear DNA substrates, its ability to authorize subsequent steps of MMR, such as MutH endonuclease activation, is almost abolished. These findings shed light on prerequisites for MutS interactions with other MMR proteins for repairing the appropriate DNA strand. PMID:22367846

Taxonomy of multi-focal nematode image stacks by a CNN based image fusion approach.

PubMed

Liu, Min; Wang, Xueping; Zhang, Hongzhong

2018-03-01

In the biomedical field, digital multi-focal images are very important for documentation and communication of specimen data, because the morphological information for a transparent specimen can be captured in form of a stack of high-quality images. Given biomedical image stacks containing multi-focal images, how to efficiently extract effective features from all layers to classify the image stacks is still an open question. We present to use a deep convolutional neural network (CNN) image fusion based multilinear approach for the taxonomy of multi-focal image stacks. A deep CNN based image fusion technique is used to combine relevant information of multi-focal images within a given image stack into a single image, which is more informative and complete than any single image in the given stack. Besides, multi-focal images within a stack are fused along 3 orthogonal directions, and multiple features extracted from the fused images along different directions are combined by canonical correlation analysis (CCA). Because multi-focal image stacks represent the effect of different factors - texture, shape, different instances within the same class and different classes of objects, we embed the deep CNN based image fusion method within a multilinear framework to propose an image fusion based multilinear classifier. The experimental results on nematode multi-focal image stacks demonstrated that the deep CNN image fusion based multilinear classifier can reach a higher classification rate (95.7%) than that by the previous multilinear based approach (88.7%), even we only use the texture feature instead of the combination of texture and shape features as in the previous work. The proposed deep CNN image fusion based multilinear approach shows great potential in building an automated nematode taxonomy system for nematologists. It is effective to classify multi-focal image stacks. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrated fuel cell stack shunt current prevention arrangement

DOEpatents

Roche, Robert P.; Nowak, Michael P.

1992-01-01

A fuel cell stack includes a plurality of fuel cells juxtaposed with one another in the stack and each including a pair of plate-shaped anode and cathode electrodes that face one another, and a quantity of liquid electrolyte present at least between the electrodes. A separator plate is interposed between each two successive electrodes of adjacent ones of the fuel cells and is unified therewith into an integral separator plate. Each integral separator plate is provided with a circumferentially complete barrier that prevents flow of shunt currents onto and on an outer peripheral surface of the separator plate. This barrier consists of electrolyte-nonwettable barrier members that are accommodated, prior to the formation of the integral separator plate, in corresponding edge recesses situated at the interfaces between the electrodes and the separator plate proper. Each barrier member extends over the entire length of the associated marginal portion and is flush with the outer periphery of the integral separator plate. This barrier also prevents cell-to-cell migration of any electrolyte that may be present at the outer periphery of the integral separator plate while the latter is incorporated in the fuel cell stack.

Two Topologically Distinct Dirac-Line Semimetal Phases and Topological Phase Transitions in Rhombohedrally Stacked Honeycomb Lattices

NASA Astrophysics Data System (ADS)

Hyart, T.; Ojajärvi, R.; Heikkilä, T. T.

2018-04-01

Three-dimensional topological semimetals can support band crossings along one-dimensional curves in the momentum space (nodal lines or Dirac lines) protected by structural symmetries and topology. We consider rhombohedrally (ABC) stacked honeycomb lattices supporting Dirac lines protected by time-reversal, inversion and spin rotation symmetries. For typical band structure parameters there exists a pair of nodal lines in the momentum space extending through the whole Brillouin zone in the stacking direction. We show that these Dirac lines are topologically distinct from the usual Dirac lines which form closed loops inside the Brillouin zone. In particular, an energy gap can be opened only by first merging the Dirac lines going through the Brillouin zone in a pairwise manner so that they turn into closed loops inside the Brillouin zone, and then by shrinking these loops into points. We show that this kind of topological phase transition can occur in rhombohedrally stacked honeycomb lattices by tuning the ratio of the tunneling amplitudes in the directions perpendicular and parallel to the layers. We also discuss the properties of the surface states in the different phases of the model.

Genotoxicity of Tri- and Hexavalent Chromium Compounds In Vivo and Their Modes of Action on DNA Damage In Vitro

PubMed Central

Fang, Zhijia; Zhao, Min; Zhen, Hong; Chen, Lifeng; Shi, Ping; Huang, Zhiwei

2014-01-01

Chromium occurs mostly in tri- and hexavalent states in the environment. Hexavalent chromium [Cr(VI)] compounds are extensively used in diverse industries, and trivalent chromium [Cr(III)] salts are used as micronutrients and dietary supplements. In the present work, we report that they both induce genetic mutations in yeast cells. They both also cause DNA damage in both yeast and Jurkat cells and the effect of Cr(III) is greater than that of Cr(VI). We further show that Cr(III) and Cr(VI) cause DNA damage through different mechanisms. Cr(VI) intercalates DNA and Cr(III) interferes base pair stacking. Based on our results, we conclude that Cr(III) can directly cause genotoxicity in vivo. PMID:25111056

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru; Vedernikov, A. I.; Sazonov, S. K.

The crystal packing of a number of styryl dyes of the pyridine series is analyzed. The structures of three dyes and three [2 + 2] photocycloaddition (PCA) products, 1,2,3,4-tetrasubstituted cyclobutanes, obtained in single crystals are determined by X-ray diffraction. Stacks of planar organic cations are characteristic of styryl dye packings. The proceeding of the PCA reaction as a single crystal-to-single crystal transformation in the syn head-to-head stacks is in principle impossible. The syn head-to-tail stacking packings are favorable for the PCA reactions resulting in the centrosymmetric rctt isomers of cyclobutane. The stacking packings, in which molecules are related by themore » twofold axes (the anti arrangement of molecules), are also favorable for PCA in single crystals. In this case, the products are the rtct isomers of cyclobutane. The presence of the I{sup -} counterions in a packing is a factor impeding the PCA reaction, because the secondary I-H-C bonds increase the rigidity of the crystal lattice. The conditions necessary for proceeding the PCA reactions in styryl dyes as single crystal-to-single crystal processes are as follows: (1) the stacks split into pairs of organic cations (dimers) with the d distances within 4.2 A in a dimer and d exceeding 4.2 A between the dimers; and (2) the dimers are surrounded by flexible shells consisting of anions, solvate molecules, or flexible moieties of the organic cations themselves.« less

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

PubMed Central

Shieh, H S; Berman, H M; Dabrow, M; Neidle, S

1980-01-01

A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry. PMID:7355129

Mirror mount

DOEpatents

Kuklo, T.C.; Bender, D.A.

1994-10-04

A unique lens or mirror mount having adjustable constraints at two key locations to allow for ''X'' and ''Y'' tilts of the mirror only is disclosed. The device uses two pair of flexures of a type such that the pivots of the mirror gimble are rigidly fixed in all planes allowing the device to have zero stacking tolerance and zero wear over time. 4 figs.

Laser-assisted atom probe tomography of four paired poly-Si/SiO2 multiple-stacks with each thickness of 10 nm

NASA Astrophysics Data System (ADS)

Kwak, C.-M.; Seol, J.-B.; Kim, Y.-T.; Park, C.-G.

2017-02-01

For the past 10 years, laser-assisted atom probe tomography (APT) analysis has been performed to quantify the near-atomic scale distribution of elements and their local chemical compositions within interfaces that determine the design, processing, and properties of virtually all materials. However, the nature of the occurring laser-induced emission at the surface of needle-shaped sample is highly complex and it has been an ongoing challenge to understand the surface-related interactions between laser-sources and tips containing non-conductive oxides for a robust and reliable analysis of multiple-stacked devices. Here, we find that the APT analysis of four paired poly-Si/SiO2 (conductive/non-conductive) multiple stacks with each thickness of 10 nm is governed by experimentally monitoring three experimental conditions, such as laser-beam energies ranged from 30 to 200 nJ, analysis temperatures varying with 30-100 K, and the inclination of aligned interfaces within a given tip toward analysis direction. Varying with laser-energy and analysis temperature, a drastic compositional ratio of doubly charged Si ions to single charged Si ions within conductive poly-Si layers is modified, as compared with ones detected in the non-conductive layers. Severe distorted APT images of multiple stacks are also inevitable, especially at the conductive layers, and leading to a lowering of the successful analysis yields. This lower throughput has been overcome though changing the inclination of interfaces within a given tip to analysis direction (planar interfaces parallel to the tip axis), but significant deviations in chemical compositions of a conductive layer counted from those of tips containing planar interfaces perpendicular to the tip axis are unavoidable owing to the Si2, SiH2O, and Si2O ions detected, for the first time, within poly-Si layers.

Investigation of Ruthenium Dissolution in Advanced Membrane Electrode Assemblies for Direct Methanol Based Fuel Cells Stacks

NASA Technical Reports Server (NTRS)

Valdez, T. I.; Firdosy, S.; Koel, B. E.; Narayanan, S. R.

2005-01-01

This viewgraph presentation gives a detailed review of the Direct Methanol Based Fuel Cell (DMFC) stack and investigates the Ruthenium that was found at the exit of the stack. The topics include: 1) Motivation; 2) Pathways for Cell Degradation; 3) Cell Duration Testing; 4) Duration Testing, MEA Analysis; and 5) Stack Degradation Analysis.

Monitoring of surface deformation in open pit mine using DInSAR time-series: a case study in the N5W iron mine (Carajás, Brazil) using TerraSAR-X data

NASA Astrophysics Data System (ADS)

Mura, José C.; Paradella, Waldir R.; Gama, Fabio F.; Santos, Athos R.; Galo, Mauricio; Camargo, Paulo O.; Silva, Arnaldo Q.; Silva, Guilherme G.

2014-10-01

We present an investigation of surface deformation using Differential SAR Interferometry (DInSAR) time-series carried out in an active open pit iron mine, the N5W, located in the Carajás Mineral Province (Brazilian Amazon region), using 33 TerraSAR-X (TSX-1) scenes. This mine has presented a historical of instability and surface monitoring measurements over sectors of the mine (pit walls) have been done based on ground based radar. Two complementary approaches were used: the standard DInSAR configuration, as an early warning of the slope instability conditions, and the DInSAR timeseries analysis. In order to decrease the topographic phase error a high resolution DEM was generated based on a stereo GeoEye-1 pair. Despite the fact that a DinSAR contains atmospheric and topographic phase artifacts and noise, it was possible to detect deformation in some interferometric pairs, covering pit benches, road ramps and waste piles. The timeseries analysis was performed using the 31 interferometric pairs, which were selected based on the highest mean coherence of a stack of 107 interferograms, presenting less phase unwrapping errors. The time-series deformation was retrieved by the Least-Squares (LS) solution using an extension of the Singular Value Decomposition (SVD), with a set of additional weighted constrain on the acceleration deformation. The atmospheric phase artifacts were filtered in the space-time domain and the DEM height errors were estimated based on the normal baseline diversity. The DInSAR time-series investigation showed good results for monitoring surface displacement in the N5W mine located in a tropical rainforest environment, providing very useful information about the ground movement for alarm, planning and risk assessment.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Disorder-controlled superconductivity at YBa2Cu3O7/SrTiO3 interfaces

NASA Astrophysics Data System (ADS)

Garcia-Barriocanal, J.; Perez-Muñoz, A. M.; Sefrioui, Z.; Arias, D.; Varela, M.; Leon, C.; Pennycook, S. J.; Santamaria, J.

2013-06-01

We examine the effect of interface disorder in suppressing superconductivity in coherently grown ultrathin YBa2Cu3O7 (YBCO) layers on SrTiO3 (STO) in YBCO/STO superlattices. The termination plane of the STO is TiO2 and the CuO chains are missing at the interface. Disorder (steps) at the STO interface cause alterations of the stacking sequence of the intracell YBCO atomic layers. Stacking faults give rise to antiphase boundaries which break the continuity of the CuO2 planes and depress superconductivity. We show that superconductivity is directly controlled by interface disorder outlining the importance of pair breaking and localization by disorder in ultrathin layers.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

PubMed Central

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.; de Pablo, Juan J.

2013-01-01

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642

Anionic silicate organic frameworks constructed from hexacoordinate silicon centres

NASA Astrophysics Data System (ADS)

Roeser, Jérôme; Prill, Dragica; Bojdys, Michael J.; Fayon, Pierre; Trewin, Abbie; Fitch, Andrew N.; Schmidt, Martin U.; Thomas, Arne

2017-10-01

Crystalline frameworks composed of hexacoordinate silicon species have thus far only been observed in a few high pressure silicate phases. By implementing reversible Si-O chemistry for the crystallization of covalent organic frameworks, we demonstrate the simple one-pot synthesis of silicate organic frameworks based on octahedral dianionic SiO6 building units. Clear evidence of the hexacoordinate environment around the silicon atoms is given by 29Si nuclear magnetic resonance analysis. Characterization by high-resolution powder X-ray diffraction, density functional theory calculation and analysis of the pair-distribution function showed that those anionic frameworks—M2[Si(C16H10O4)1.5], where M = Li, Na, K and C16H10O4 is 9,10-dimethylanthracene-2,3,6,7-tetraolate—crystallize as two-dimensional hexagonal layers stabilized in a fully eclipsed stacking arrangement with pronounced disorder in the stacking direction. Permanent microporosity with high surface area (up to 1,276 m2 g-1) was evidenced by gas-sorption measurements. The negatively charged backbone balanced with extra-framework cations and the permanent microporosity are characteristics that are shared with zeolites.

Zebra Finch Mates Use Their Forebrain Song System in Unlearned Call Communication

PubMed Central

Ter Maat, Andries; Trost, Lisa; Sagunsky, Hannes; Seltmann, Susanne; Gahr, Manfred

2014-01-01

Unlearned calls are produced by all birds whereas learned songs are only found in three avian taxa, most notably in songbirds. The neural basis for song learning and production is formed by interconnected song nuclei: the song control system. In addition to song, zebra finches produce large numbers of soft, unlearned calls, among which “stack” calls are uttered frequently. To determine unequivocally the calls produced by each member of a group, we mounted miniature wireless microphones on each zebra finch. We find that group living paired males and females communicate using bilateral stack calling. To investigate the role of the song control system in call-based male female communication, we recorded the electrical activity in a premotor nucleus of the song control system in freely behaving male birds. The unique combination of acoustic monitoring together with wireless brain recording of individual zebra finches in groups shows that the neuronal activity of the song system correlates with the production of unlearned stack calls. The results suggest that the song system evolved from a brain circuit controlling simple unlearned calls to a system capable of producing acoustically rich, learned vocalizations. PMID:25313846

Ares I-X Flight Test Vehicle Modal Test

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Templeton, Justin D.; Reaves, Mercedes C.; Horta, Lucas G.; Gaspar, James L.; Bartolotta, Paul A.; Parks, Russel A.; Lazor, Daniel R.

2010-01-01

The first test flight of NASA's Ares I crew launch vehicle, called Ares I-X, was launched on October 28, 2009. Ares I-X used a 4-segment reusable solid rocket booster from the Space Shuttle heritage with mass simulators for the 5th segment, upper stage, crew module and launch abort system. Flight test data will provide important information on ascent loads, vehicle control, separation, and first stage reentry dynamics. As part of hardware verification, a series of modal tests were designed to verify the dynamic finite element model (FEM) used in loads assessments and flight control evaluations. Based on flight control system studies, the critical modes were the first three free-free bending mode pairs. Since a test of the free-free vehicle was not practical within project constraints, modal tests for several configurations during vehicle stacking were defined to calibrate the FEM. Test configurations included two partial stacks and the full Ares I-X flight test vehicle on the Mobile Launcher Platform. This report describes the test requirements, constraints, pre-test analysis, test execution and results for the Ares I-X flight test vehicle modal test on the Mobile Launcher Platform. Initial comparisons between pre-test predictions and test data are also presented.

Multi-scale comparison of source parameter estimation using empirical Green's function approach

NASA Astrophysics Data System (ADS)

Chen, X.; Cheng, Y.

2015-12-01

Analysis of earthquake source parameters requires correction of path effect, site response, and instrument responses. Empirical Green's function (EGF) method is one of the most effective methods in removing path effects and station responses by taking the spectral ratio between a larger and smaller event. Traditional EGF method requires identifying suitable event pairs, and analyze each event individually. This allows high quality estimations for strictly selected events, however, the quantity of resolvable source parameters is limited, which challenges the interpretation of spatial-temporal coherency. On the other hand, methods that exploit the redundancy of event-station pairs are proposed, which utilize the stacking technique to obtain systematic source parameter estimations for a large quantity of events at the same time. This allows us to examine large quantity of events systematically, facilitating analysis of spatial-temporal patterns, and scaling relationship. However, it is unclear how much resolution is scarified during this process. In addition to the empirical Green's function calculation, choice of model parameters and fitting methods also lead to biases. Here, using two regional focused arrays, the OBS array in the Mendocino region, and the borehole array in the Salton Sea geothermal field, I compare the results from the large scale stacking analysis, small-scale cluster analysis, and single event-pair analysis with different fitting methods to systematically compare the results within completely different tectonic environment, in order to quantify the consistency and inconsistency in source parameter estimations, and the associated problems.

Myristoylation Restricts Orientation of the GRASP Domain on Membranes and Promotes Membrane Tethering*

PubMed Central

Heinrich, Frank; Nanda, Hirsh; Goh, Haw Zan; Bachert, Collin; Lösche, Mathias; Linstedt, Adam D.

2014-01-01

The mammalian Golgi reassembly stacking protein (GRASP) proteins are Golgi-localized homotypic membrane tethers that organize Golgi stacks into a long, contiguous ribbon-like structure. It is unknown how GRASPs undergo trans pairing given that cis interactions between the proteins in the plane of the membrane are intrinsically favored. To test the hypothesis that myristoylation of the self-interacting GRASP domain restricts its orientation on the membrane to favor trans pairing, we established an in vitro assay that recapitulates GRASP-dependent membrane tethering and used neutron reflection under similar conditions to determine the orientation of the GRASP domain. In vivo, the membrane association of GRASP proteins is conferred by the simultaneous insertion of an N-terminal myristic acid and binding to a Golgi-associated binding partner. In our assay, the latter contact was replaced using a C-terminal hexa-His moiety, which bound to Ni2+-conjugated lipids incorporated into a substrate-supported bilayer lipid membrane. Nonmyristoylated protein lacked a fixed orientation on the membrane and inefficiently tethered liposomes. In contrast, myristoylated GRASP promoted tethering and exhibited a unique membrane complex. Thus, myristoylation restricts the membrane orientation of the GRASP domain favoring interactions in trans for membrane tethering. PMID:24505136

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions.

PubMed

Tauer, Tony P; Sherrill, C David

2005-11-24

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.

PRELIMINARY RESULTS OF THE AGC-4 IRRADIATION IN THE ADVANCED TEST REACTOR AND DESIGN OF AGC-5 (HTR16-18469)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davenport, Michael; Petti, D. A.

The United States Department of Energy’s Advanced Reactor Technologies (ART) Program will irradiate up to six nuclear graphite creep experiments in the Advanced Test Reactor (ATR) located at the Idaho National Laboratory (INL). The graphite experiments are being irradiated over an approximate eight year period to support development of a graphite irradiation performance data base on the new nuclear grade graphites now available for use in high temperature gas reactors. The goals of the irradiation experiments are to obtain irradiation performance data, including irradiation creep, at different temperatures and loading conditions to support design of the Very High Temperature Gasmore » Reactor (VHTR), as well as other future gas reactors. The experiments each consist of a single capsule that contain six stacks of graphite specimens, with half of the graphite specimens in each stack under a compressive load, while the other half of the specimens are not be subjected to a compressive load during irradiation. The six stacks have differing compressive loads applied to the top half of diametrically opposite pairs of specimen stacks. A seventh specimen stack in the center of the capsule does not have a compressive load. The specimens are being irradiated in an inert sweep gas atmosphere with on-line temperature and compressive load monitoring and control. There are also samples taken of the sweep gas effluent to measure any oxidation or off-gassing of the specimens that may occur during initial start-up of the experiment. The first experiment, AGC-1, started its irradiation in September 2009, and the irradiation was completed in January 2011. The second experiment, AGC-2, started its irradiation in April 2011 and completed its irradiation in May 2012. The third experiment, AGC-3, started its irradiation in late November 2012 and completed in the April of 2014. AGC-4 is currently being irradiated in the ATR. This paper will briefly discuss the preliminary irradiation results of the AGC-4 experiment, as well as the design of AGC-5.« less

Analysis of transthoracic impedance during real cardiac arrest defibrillation attempts in older children and adolescents: are stacked-shocks appropriate?

PubMed

Niles, Dana E; Nishisaki, Akira; Sutton, Robert M; Brunner, Sara; Stavland, Mette; Mahadevaiah, Shruthi; Meaney, Peter A; Maltese, Matthew R; Berg, Robert A; Nadkarni, Vinay M

2010-11-01

In 2005, the AHA changed the treatment recommendation for shockable rhythms from 3 transthoracic stacked-shocks to a single shock followed by immediate chest compressions. The stacked-shock recommendation was based on low first-shock efficacy of monophasic waveforms and the theoretical decrease in transthoracic impedance (TTI) following each shock. The objective of this study was to characterize TTI following biphasic defibrillation attempts in children ≥ 8 yrs during cardiac arrest to assess whether a stacked-shock approach may be appropriate to improve defibrillation success. TTI (Ohms (Ω)) was collected via standard anterior-apical defibrillator electrode pads during consecutive in-hospital cardiac arrest biphasic defibrillation attempts in children ≥ 8 yrs. Analytic data points for TTI were: 0.1s pre-shock (baseline); post-shock at 0.1, 0.5, 1.0, 1.5, and 2.0 s. TTI variables analyzed with descriptive summaries/paired t-test. p values < 0.05 considered statistically significant after correction for multiple comparisons. Analysis yielded 13 evaluable shock events during 5 cardiac arrests (mean age 14.3 ± 5 yrs, weight 47.4 ± 7.3 kg) between September 2006 and May 2009. Compared to 0.1s pre-shock baseline values (56.8 ± 23.4 Ω), TTI was significantly lower immediately 0.1s post-shock (55.2 ± 22.2 Ω, p = 0.003). Post-shock mean difference from baseline was 1.6 Ω at 0.1s (p = 0.015), 1.4 Ω at 0.5s (p = 0.019) 1.4 Ω at 1.0 s (p = 0.023), 1.1 Ω at 1.5 s (p = 0.028), and 0.95 Ω at 2.0 s (p = 0.096). Time to recharge our clinical defibrillators to standard biphasic shock dose was 2.80 ± 0.05 s. During cardiac arrests in children ≥ 8 yrs, TTI decreased after biphasic shocks, but the limited magnitude and duration of TTI changes suggest that stacked-shocks would not improve defibrillation success. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes.

PubMed

Patel, D J; Canuel, L L

1977-07-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

PubMed Central

Patel, Dinshaw J.; Canuel, Lita L.

1977-01-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. PMID:268613

Anomalous resonances of an optical microcavity with a hyperbolic metamaterial core

NASA Astrophysics Data System (ADS)

Travkin, Evgenij; Kiel, Thomas; Sadofev, Sergey; Busch, Kurt; Benson, Oliver; Kalusniak, Sascha

2018-05-01

We embed a hyperbolic metamaterial based on stacked layer pairs of epitaxially grown ZnO/ZnO:Ga in a monolithic optical microcavity, and we investigate the arising unique resonant effects experimentally and theoretically. Unlike traditional metals, the semiconductor-based approach allows us to utilize all three permittivity regions of the hyperbolic metamaterial in the near-infrared spectral range. This configuration gives rise to modes of identical orders appearing at different frequencies, a zeroth-order resonance in an all-positive permittivity region, and a continuum of high-order modes. In addition, an unusual lower cutoff frequency is introduced to the resonator mode spectrum. The observed effects expand the possibilities for customization of optical resonators; in particular, the zeroth-order and high-order modes hold strong potential for the realization of deeply subwavelength cavity sizes.

Manipulation of double-stranded DNA melting by force

NASA Astrophysics Data System (ADS)

Singh, Amit Raj; Granek, Rony

2017-09-01

By integrating elasticity—as described by the Gaussian network model—with bond binding energies that distinguish between different base-pair identities and stacking configurations, we study the force induced melting of a double-stranded DNA (dsDNA). Our approach is a generalization of our previous study of thermal dsDNA denaturation [J. Chem. Phys. 145, 144101 (2016), 10.1063/1.4964285] to that induced by force at finite temperatures. It allows us to obtain semimicroscopic information about the opening of the chain, such as whether the dsDNA opens from one of the ends or from the interior, forming an internal bubble. We study different types of force manipulation: (i) "end unzipping," with force acting at a single end base pair perpendicular to the helix, (ii) "midunzipping," with force acting at a middle base pair perpendicular to the helix, and (iii) "end shearing," where the force acts at opposite ends along the helix. By monitoring the free-energy landscape and probability distribution of intermediate denaturation states, we show that different dominant intermediate states are stabilized depending on the type of force manipulation used. In particular, the bubble state of the sequence L60B36, which we have previously found to be a stable state during thermal denaturation, is absent for end unzipping and end shearing, whereas very similar bubbles are stabilized by midunzipping, or when the force location is near the middle of the chain. Ours results offer a simple tool for stabilizing bubbles and loops using force manipulations at different temperatures, and may implicate on the mechanism in which DNA enzymes or motors open regions of the chain.

Electronic structure and pair potential energy analysis of 4-n-methoxy-4′-cyanobiphenyl: A nematic liquid crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Dipendra, E-mail: d-11sharma@rediffmail.com; Tiwari, S. N., E-mail: sntiwari123@rediffmail.com; Dwivedi, M. K., E-mail: dwivedi-ji@gmail.com

2016-05-06

Electronic structure properties of 4-n-methoxy-4′-cyanobiphenyl, a pure nematic liquid crystal have been examined using an ab‒initio, HF/6‒31G(d,p) technique with GAMESS program. Conformational and charge distribution analysis have been carried out. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the liquid crystal molecule have been calculated. Further, stacking, side by side and end to end interactions between a molecular pair have been evaluated. Results have been used to elucidate the physico-chemical and liquid crystalline properties of the system.

A big data geospatial analytics platform - Physical Analytics Integrated Repository and Services (PAIRS)

NASA Astrophysics Data System (ADS)

Hamann, H.; Jimenez Marianno, F.; Klein, L.; Albrecht, C.; Freitag, M.; Hinds, N.; Lu, S.

2015-12-01

A big data geospatial analytics platform:Physical Analytics Information Repository and Services (PAIRS)Fernando Marianno, Levente Klein, Siyuan Lu, Conrad Albrecht, Marcus Freitag, Nigel Hinds, Hendrik HamannIBM TJ Watson Research Center, Yorktown Heights, NY 10598A major challenge in leveraging big geospatial data sets is the ability to quickly integrate multiple data sources into physical and statistical models and be run these models in real time. A geospatial data platform called Physical Analytics Information and Services (PAIRS) is developed on top of open source hardware and software stack to manage Terabyte of data. A new data interpolation and re gridding is implemented where any geospatial data layers can be associated with a set of global grid where the grid resolutions is doubling for consecutive layers. Each pixel on the PAIRS grid have an index that is a combination of locations and time stamp. The indexing allow quick access to data sets that are part of a global data layers and allowing to retrieve only the data of interest. PAIRS takes advantages of parallel processing framework (Hadoop) in a cloud environment to digest, curate, and analyze the data sets while being very robust and stable. The data is stored on a distributed no-SQL database (Hbase) across multiple server, data upload and retrieval is parallelized where the original analytics task is broken up is smaller areas/volume, analyzed independently, and then reassembled for the original geographical area. The differentiating aspect of PAIRS is the ability to accelerate model development across large geographical regions and spatial resolution ranging from 0.1 m up to hundreds of kilometer. System performance is benchmarked on real time automated data ingestion and retrieval of Modis and Landsat data layers. The data layers are curated for sensor error, verified for correctness, and analyzed statistically to detect local anomalies. Multi-layer query enable PAIRS to filter different data layers based on specific conditions (e.g analyze flooding risk of a property based on topography, soil ability to hold water, and forecasted precipitation) or retrieve information about locations that share similar weather and vegetation patterns during extreme weather events like heat wave.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

PubMed

Martinez, Hugo M; Maizel, Jacob V; Shapiro, Bruce A

2008-06-01

Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

PubMed Central

Kirouac, Kevin N.; Basu, Ashis K.; Ling, Hong

2013-01-01

Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene–derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. Polι maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson–Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polη prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer. PMID:23268450

Evolving a polymerase for hydrophobic base analogues.

PubMed

Loakes, David; Gallego, José; Pinheiro, Vitor B; Kool, Eric T; Holliger, Philipp

2009-10-21

Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.

Bragg reflector based gate stack architecture for process integration of excimer laser annealing

NASA Astrophysics Data System (ADS)

Fortunato, G.; Mariucci, L.; Cuscunà, M.; Privitera, V.; La Magna, A.; Spinella, C.; Magrı, A.; Camalleri, M.; Salinas, D.; Simon, F.; Svensson, B.; Monakhov, E.

2006-12-01

An advanced gate stack structure, which incorporates a Bragg reflector, has been developed for the integration of excimer laser annealing into the power metal-oxide semiconductor (MOS) transistor fabrication process. This advanced gate structure effectively protects the gate stack from melting, thus solving the problem related to protrusion formation. By using this gate stack configuration, power MOS transistors were fabricated with improved electrical characteristics. The Bragg reflector based gate stack architecture can be applied to other device structures, such as scaled MOS transistors, thus extending the possibilities of process integration of excimer laser annealing.

Prolonging fuel cell stack lifetime based on Pontryagin's Minimum Principle in fuel cell hybrid vehicles and its economic influence evaluation

NASA Astrophysics Data System (ADS)

Zheng, C. H.; Xu, G. Q.; Park, Y. I.; Lim, W. S.; Cha, S. W.

2014-02-01

The lifetime of fuel cell stacks is a major issue currently, especially for automotive applications. In order to take into account the lifetime of fuel cell stacks while considering the fuel consumption minimization in fuel cell hybrid vehicles (FCHVs), a Pontryagin's Minimum Principle (PMP)-based power management strategy is proposed in this research. This strategy has the effect of prolonging the lifetime of fuel cell stacks. However, there is a tradeoff between the fuel cell stack lifetime and the fuel consumption when this strategy is applied to an FCHV. Verifying the positive economic influence of this strategy is necessary in order to demonstrate its superiority. In this research, the economic influence of the proposed strategy is assessed according to an evaluating cost which is dependent on the fuel cell stack cost, the hydrogen cost, the fuel cell stack lifetime, and the lifetime prolonging impact on the fuel cell stack. Simulation results derived from the proposed power management strategy are also used to evaluate the economic influence. As a result, the positive economic influence of the proposed PMP-based power management strategy is proved for both current and future FCHVs.

A Review of the CMOS Buried Double Junction (BDJ) Photodetector and its Applications

PubMed Central

Feruglio, Sylvain; Lu, Guo-Neng; Garda, Patrick; Vasilescu, Gabriel

2008-01-01

A CMOS Buried Double Junction PN (BDJ) photodetector consists of two vertically-stacked photodiodes. It can be operated as a photodiode with improved performance and wavelength-sensitive response. This paper presents a review of this device and its applications. The CMOS implementation and operating principle are firstly described. This includes the description of several key aspects directly related to the device performances, such as surface reflection, photon absorption and electron-hole pair generation, photocurrent and dark current generation, etc. SPICE modelling of the detector is then presented. Next, design and process considerations are proposed in order to improve the BDJ performance. Finally, several BDJ-detector-based image sensors provide a survey of their applications. PMID:27873887

Synthesis Characterization and DNA Interaction Studies of a New Zn(II) Complex Containing Different Dinitrogen Aromatic Ligands

PubMed Central

Shahabadi, Nahid; Mohammadi, Somaye

2012-01-01

A mononuclear complex of Zn(II), [Zn(DIP)2 (DMP)] (NO3)2 ·2H2O in which DIP is 4,7-diphenyl-1,10-phenanthroline and DMP is 4,4′-dimethyl-2,2′-bipyridine has been prepared and characterized by 1HNMR spectroscopy, FT-IR, UV-Vis and elemental analysis techniques. DNA-binding properties of the complex were studied using UV-vis spectra, circular dichroism (CD) spectra, fluorescence, cyclic voltammetry (CV), and viscosity measurements. The results indicate that this zinc(II) complex can intercalate into the stacked base pairs of DNA and compete with the strong intercalator ethidium bromide for the intercalative binding sites. PMID:22956919

A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple.

PubMed

Kuryavyi, V; Majumdar, A; Shallop, A; Chernichenko, N; Skripkin, E; Jones, R; Patel, D J

2001-06-29

The architecture of G-G-G-G tetrad-aligned DNA quadruplexes in monovalent cation solution is dependent on the directionality of the four strands, which in turn are defined by loop connectivities and the guanine syn/anti distribution along individual strands and within individual G-G-G-G tetrads. The smallest unimolecular G-quadruplex belongs to the d(G2NnG2NnG2NnG2) family, which has the potential to form two stacked G-tetrads linked by Nn loop connectivities. Previous studies have focused on the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), where Nn was T2 for the first and third connecting loops and TGT for the middle connecting loop. This DNA aptamer in K(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(anti)-G(syn)-G(anti) tetrads, adjacent strands which are antiparallel to each other and edge-wise connecting T2, TGT and T2 loops. We now report on the NMR-based solution structure of the d(G2T4G2CAG2GT4G2T) sequence, which differs from the thrombin-binding DNA aptamer sequence in having longer first (T4) and third (GT4) loops and a shorter (CA) middle loop. This d(G2T4G2CAG2GT4G2T) sequence in Na(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads, adjacent strands which have one parallel and one antiparallel neighbors and distinct non-edge-wise loop connectivities. Specifically, the longer first (T4) and third (GT4) loops are of the diagonal type while the shorter middle loop is of the double chain reversal type. In addition, the pair of stacked G-G-G-G tetrads are flanked on one side by a G-(T-T) triad and on the other side by a T-T-T triple. The distinct differences in strand directionalities, loop connectivities and syn/anti distribution within G-G-G-G tetrads between the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic nature of higher-order DNA architectures. Further, these two small unimolecular G-quadruplexes, which are distinct from each other and from parallel-stranded G-quadruplexes, provide novel targets for ligand recognition. Our results demonstrate that the double chain reversal loop connectivity identified previously by our laboratory within the Tetrahymena telomere d(T2G4)4 quadruplex, is a robust folding topology, since it has now also been observed within the d(G2T4G2CAG2GT4G2T) quadruplex. The identification of a G-(T-T) triad and a T-T-T triple, expands on the available recognition alignments for base triads and triples. Copyright 2001 Academic Press.

Graphite-based photovoltaic cells

DOEpatents

Lagally, Max; Liu, Feng

2010-12-28

The present invention uses lithographically patterned graphite stacks as the basic building elements of an efficient and economical photovoltaic cell. The basic design of the graphite-based photovoltaic cells includes a plurality of spatially separated graphite stacks, each comprising a plurality of vertically stacked, semiconducting graphene sheets (carbon nanoribbons) bridging electrically conductive contacts.

User Driven Image Stacking for ODI Data and Beyond via a Highly Customizable Web Interface

NASA Astrophysics Data System (ADS)

Hayashi, S.; Gopu, A.; Young, M. D.; Kotulla, R.

2015-09-01

While some astronomical archives have begun serving standard calibrated data products, the process of producing stacked images remains a challenge left to the end-user. The benefits of astronomical image stacking are well established, and dither patterns are recommended for almost all observing targets. Some archives automatically produce stacks of limited scientific usefulness without any fine-grained user or operator configurability. In this paper, we present PPA Stack, a web based stacking framework within the ODI - Portal, Pipeline, and Archive system. PPA Stack offers a web user interface with built-in heuristics (based on pointing, filter, and other metadata information) to pre-sort images into a set of likely stacks while still allowing the user or operator complete control over the images and parameters for each of the stacks they wish to produce. The user interface, designed using AngularJS, provides multiple views of the input dataset and parameters, all of which are synchronized in real time. A backend consisting of a Python application optimized for ODI data, wrapped around the SWarp software, handles the execution of stacking workflow jobs on Indiana University's Big Red II supercomputer, and the subsequent ingestion of the combined images back into the PPA archive. PPA Stack is designed to enable seamless integration of other stacking applications in the future, so users can select the most appropriate option for their science.

Recognition of platinum-DNA adducts by HMGB1a.

PubMed

Ramachandran, Srinivas; Temple, Brenda; Alexandrova, Anastassia N; Chaney, Stephen G; Dokholyan, Nikolay V

2012-09-25

Cisplatin (CP) and oxaliplatin (OX), platinum-based drugs used widely in chemotherapy, form adducts on intrastrand guanines (5'GG) in genomic DNA. DNA damage recognition proteins, transcription factors, mismatch repair proteins, and DNA polymerases discriminate between CP- and OX-GG DNA adducts, which could partly account for differences in the efficacy, toxicity, and mutagenicity of CP and OX. In addition, differential recognition of CP- and OX-GG adducts is highly dependent on the sequence context of the Pt-GG adduct. In particular, DNA binding protein domain HMGB1a binds to CP-GG DNA adducts with up to 53-fold greater affinity than to OX-GG adducts in the TGGA sequence context but shows much smaller differences in binding in the AGGC or TGGT sequence contexts. Here, simulations of the HMGB1a-Pt-DNA complex in the three sequence contexts revealed a higher number of interface contacts for the CP-DNA complex in the TGGA sequence context than in the OX-DNA complex. However, the number of interface contacts was similar in the TGGT and AGGC sequence contexts. The higher number of interface contacts in the CP-TGGA sequence context corresponded to a larger roll of the Pt-GG base pair step. Furthermore, geometric analysis of stacking of phenylalanine 37 in HMGB1a (Phe37) with the platinated guanines revealed more favorable stacking modes correlated with a larger roll of the Pt-GG base pair step in the TGGA sequence context. These data are consistent with our previous molecular dynamics simulations showing that the CP-TGGA complex was able to sample larger roll angles than the OX-TGGA complex or either CP- or OX-DNA complexes in the AGGC or TGGT sequences. We infer that the high binding affinity of HMGB1a for CP-TGGA is due to the greater flexibility of CP-TGGA compared to OX-TGGA and other Pt-DNA adducts. This increased flexibility is reflected in the ability of CP-TGGA to sample larger roll angles, which allows for a higher number of interface contacts between the Pt-DNA adduct and HMGB1a.

New t-gap insertion-deletion-like metrics for DNA hybridization thermodynamic modeling.

PubMed

D'yachkov, Arkadii G; Macula, Anthony J; Pogozelski, Wendy K; Renz, Thomas E; Rykov, Vyacheslav V; Torney, David C

2006-05-01

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. Thermodynamic distance functions are important components in the construction of DNA codes, and DNA codes are important components in biomolecular computing, nanotechnology, and other biotechnical applications that employ DNA hybridization assays. We show how our new distances can be calculated by using a dynamic programming method, and we derive a Varshamov-Gilbert-like lower bound on the size of some of codes using these distance functions as constraints. We also discuss software implementation of our DNA code design methods.

Persistent Self-Association of Solute Molecules in Solution.

PubMed

Tang, Weiwei; Mo, Huaping; Zhang, Mingtao; Parkin, Sean; Gong, Junbo; Wang, Jingkang; Li, Tonglei

2017-11-02

The structural evolvement of a solute determines the crystallization outcome. The self-association mechanism leading to nucleation, however, remains poorly understood. Our current study explored the solution chemistry of a model compound, tolfenamic acid (TFA), in three different solvents mainly by solution NMR. It was found that hydrogen-bonded pairs of solute-solute or solute-solvent stack with each through forming a much weaker π-π interaction as the concentration increases. Depending on the solvent, configurations of the solution species may be retained in the resultant crystal structure or undergo rearrangement. Yet, the π-π stacking is always retained in the crystal regardless of the solvent used for the crystallization. The finding suggests that nucleation not only involves the primary intermolecular interaction (hydrogen bonding) but also engages the secondary forces in the self-assembly process.

Linear particle accelerator with seal structure between electrodes and insulators

DOEpatents

Broadhurst, John H.

1989-01-01

An electrostatic linear accelerator includes an electrode stack comprised of primary electrodes formed or Kovar and supported by annular glass insulators having the same thermal expansion rate as the electrodes. Each glass insulator is provided with a pair of fused-in Kovar ring inserts which are bonded to the electrodes. Each electrode is designed to define a concavo-convex particle trap so that secondary charged particles generated within the accelerated beam area cannot reach the inner surface of an insulator. Each insulator has a generated inner surface profile which is so configured that the electrical field at this surface contains no significant tangential component. A spark gap trigger assembly is provided, which energizes spark gaps protecting the electrodes affected by over voltage to prevent excessive energy dissipation in the electrode stack.

Air conditioning system

DOEpatents

Lowenstein, Andrew; Miller, Jeffrey; Gruendeman, Peter; DaSilva, Michael

2005-02-01

An air conditioner comprises a plurality of plates arranged in a successively stacked configuration with portions thereof having a spaced apart arrangement, and defining between successive adjacent pairs of plates at the spaced apart portions a first and second series of discrete alternating passages wherein a first air stream is passed through the first series of passages and a second air stream is passed through the second series of passages; and said stacked configuration of plates forming integrally therewith a liquid delivery means for delivering from a source a sufficient quantity of a liquid to the inside surfaces of the first series of fluid passages in a manner which provides a continuous flow of the liquid from a first end to a second end of the plurality of plates while in contact with the first air stream.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru; Sitin, A. G.; Gulakova, E. N.

The crystal and molecular structures of five styrylheterocycles of the quinoline series are studied. All molecules are planar. The double bond in the ethylene fragment is essentially localized. In the molecule of 2-(4-methylstyryl)quinoline, the ethylene fragment is disordered by the bicycle-pedal pattern. In four of the five compounds, the crystal packings do not contain stacking dimers prearranged for the [2+2] photocycloaddition (PCA) reaction. In the crystal of 2-(3-nitrostyryl)quinoline, pairs of crystallographically independent molecules form stacking dimers. In a dimer, the ethylene fragments have a twist orientation, which is incompatible with the PCA reaction. An attempt to initiate a temperature-dependent processmore » of bicyclepedal isomerization in the crystal and, as a consequence, the PCA reaction by means of simultaneous irradiation and heating of a single crystal is unsuccessful.« less

KSC-2009-5362

NASA Image and Video Library

2009-10-07

CAPE CANAVERAL, Fla. – In the Vehicle Assembly Building's High Bay 1 at NASA’s Kennedy Space Center in Florida, workers supervise space shuttle Atlantis as it is positioned next to an external fuel tank, at left, and pair of solid rocket boosters secured to a mobile launcher platform. Next, Atlantis will be attached, completing the stacking operation. Rollout of the completed shuttle stack to Kennedy’s Launch Pad 39A, a significant milestone in launch processing activities, is planned for Oct. 13. Liftoff of Atlantis on its STS-129 mission to the International Space Station is targeted for 4:04 p.m. EST Nov. 12 during a 10-minute launch window. For information on the STS-129 mission and crew, visit http://www.nasa.gov/mission_pages/shuttle/shuttlemissions/sts129/index.html. Photo credit: NASA/Jack Pfaller

Body Doping Profile of Select Device to Minimize Program Disturbance in Three-Dimensional Stack NAND Flash Memory

NASA Astrophysics Data System (ADS)

Choe, Byeong-In; Park, Byung-Gook; Lee, Jong-Ho

2013-06-01

The program disturbance characteristic in the three-dimensional (3D) stack NAND flash was analyzed for the first time in terms of string select line (SSL) threshold voltage (Vth) and p-type body doping profile. From the edge word line (W/L) program disturbance, we can observe the boosted channel potential loss as a function of SSL Vth and body doping profile for SSL device. According to simulation work, a high Vth of the SSL device is required to suppress channel leakage during programming. When the body doping of the SSL device is high in the channel, there is a large band bending near the gate edge of the SSL adjacent to the edge W/L cell of boosted cell strings, which generates significantly electron-hole pairs. The generated electrons decreases the boosted channel potential, resulting in increase of program disturbance of the inhibit strings. Through optimization of the body doping profile of the SSL device, both channel leakage and the program disturbance are successfully suppressed for a highly reliable 3D stack NAND flash memory cell operation.

Ionic liquid-induced aggregate formation and their applications.

PubMed

Dutta, Rupam; Kundu, Sangita; Sarkar, Nilmoni

2018-06-01

In the last two decades, researchers have extensively studied highly stable and ordered supramolecular assembly formation using oppositely charged surfactants. Thereafter, surface-active ionic liquids (SAILs), a special class of room temperature ionic liquids (RTILs), replace the surfactants to form various supramolecular aggregates. Therefore, in the last decade, the building blocks of the supramolecular aggregates (micelle, mixed micelle, and vesicular assemblies) have changed from oppositely charged surfactant/surfactant pair to surfactant/SAIL and SAIL/SAIL pair. It is also found that various biomolecules can also interact with SAILs to construct biologically important supramolecular assemblies. The very latest addition to this combination of ion pairs is the dye molecules having a long hydrophobic chain part along with a hydrophilic ionic head group. Thus, dye/surfactant or dye/SAIL pair also produces different assemblies through electrostatic, hydrophobic, and π-π stacking interactions. Vesicles are one of the important self-assemblies which mimic cellular membranes, and thus have biological application as a drug carrier. Moreover, vesicles can act as a suitable microreactor for nanoparticle synthesis.

Means for limiting and ameliorating electrode shorting

DOEpatents

Van Konynenburg, Richard A.; Farmer, Joseph C.

1999-01-01

A fuse and filter arrangement for limiting and ameliorating electrode shorting in capacitive deionization water purification systems utilizing carbon aerogel, for example. This arrangement limits and ameliorates the effects of conducting particles or debonded carbon aerogel in shorting the electrodes of a system such as a capacitive deionization water purification system. This is important because of the small interelectrode spacing and the finite possibility of debonding or fragmentation of carbon aerogel in a large system. The fuse and filter arrangement electrically protect the entire system from shutting down if a single pair of electrodes is shorted and mechanically prevents a conducting particle from migrating through the electrode stack, shorting a series of electrode pairs in sequence. It also limits the amount of energy released in a shorting event. The arrangement consists of a set of circuit breakers or fuses with one fuse or breaker in the power line connected to one electrode of each electrode pair and a set of screens of filters in the water flow channels between each set of electrode pairs.

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

DOE PAGES

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; ...

2015-12-01

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

Theoretical Evidence for the Stronger Ability of Thymine to Disperse SWCNT than Cytosine and Adenine: self-stacking of DNA bases vs their cross-stacking with SWCNT

PubMed Central

Wang, Yixuan

2008-01-01

Self-stacking of four DNA bases, adenine (A), cytosine (C), guanine (G) and thymine (T), and their cross-stacking with (5,5) as well as (10,0) single walled carbon nanotubes (SWCNTs) were extensively investigated with a novel hybrid DFT method, MPWB1K/cc-pVDZ. The binding energies were further corrected with MP2/6-311++G(d,p) method in both gas phase and aqueous solution, where the solvent effects were included with conductor-like polarized continuum model (CPCM) model and UAHF radii. The strongest self-stacking of G and A takes displaced anti-parallel configuration, but un-displaced or “eclipsed” anti-parallel configuration is the most stable for C and T. In gas phase the self-stacking of nucleobases decreases in the sequence G>A>C>T, while because of quite different solvent effects their self-stacking in aqueous solution exhibits a distinct sequence A>G>T>C. For a given base, cross-stacking is stronger than self-stacking in both gas phase and aqueous solution. Binding energy for cross-stacking in gas phase varies as G>A>T>C for both (10,0) and (5,5) SWCNTs, and the binding of four nucleobases to (10,0) is slightly stronger than to (5,5) SWCNT by a range of 0.1–0.5 kcal/mol. The cross-stacking in aqueous solution varies differently from that gas phase: A>G>T>C for (10,0) SWCNT and G>A>T>C for (5,5) SWCNT. It is suggested that the ability of nucleobases to disperse SWCNT depends on relative strength (ΔΔEbinsol) of self-stacking and cross-stacking with SWCNT in aqueous solution. Of the four investigated nucleobases thymine (T) exhibits the highest (ΔΔEbinsol) which can well explain the experimental finding that T more efficiently functionalizes SWCNT than C and A. PMID:18946514

G-quadruplexes as sensing probes.

PubMed

Ruttkay-Nedecky, Branislav; Kudr, Jiri; Nejdl, Lukas; Maskova, Darina; Kizek, Rene; Adam, Vojtech

2013-11-28

Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K+, Ca2+, Ag+, Hg2+, Cu2+, Pb2+, Sr2+, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.

Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

PubMed Central

Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2007-01-01

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGGAAATTCCCG)2-3′. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches. PMID:17194756

Comparative study on sample stacking by moving reaction boundary formed with weak acid and weak or strong base in capillary electrophoresis: II. Experiments.

PubMed

Zhang, Wei; Fan, Liuyin; Shao, Jing; Li, Si; Li, Shan; Cao, Chengxi

2011-04-15

To demonstrate the theoretic method on the stacking of zwitterion with moving reaction boundary (MRB) in the accompanying paper, the relevant experiments were performed. The experimental results quantitatively show that (1) MRB velocity, including the comparisons between MRB and zwitterionic velocities, possesses key importance to the design of MRB stacking; (2) a much long front alkaline plug without sample should be injected before the sample injection for a complete stacking of zwitterion if sample buffer is prepared with strong base, conversely no such plug is needed if using a weak base as the sample buffer with proper concentration and pH value; (3) the presence of salt in MRB system holds dramatic effect on the MRB stacking if sample solution is a strong base, but has no effect if a weak alkali is used as sample solution; (4) all of the experiments of this paper, including the previous work, quantitatively manifest the theory and predictions shown in the accompanying paper. In addition, the so-called derivative MRB-induced re-stacking and transient FASI-induced re-stacking were also observed during the experiments, and the relevant mechanisms were briefly demonstrated with the results. The theory and its calculation procedures developed in the accompanying paper can be well used for the predictions to the MRB stacking of zwitterion in CE. Copyright © 2011 Elsevier B.V. All rights reserved.

Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs.

PubMed

Shahabadi, Nahid; Asadian, Ali Ashraf; Mahdavi, Mryam

2017-11-02

In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV-Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (K b = 1.4 × 10 4 M -1 ) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 -4.8 × 10 4 M -1 . CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.

A 1 kWel thermoelectric stack for geothermal power generation - Modeling and geometrical optimization

NASA Astrophysics Data System (ADS)

Suter, C.; Jovanovic, Z.; Steinfeld, A.

2012-06-01

A thermoelectric stack composed of arrays of Bi-Te alloy thermoelectric converter (TEC) modules is considered for geothermal heat conversion. The TEC modules consist of Al2O3 plates with surface 30×30 mm2 and 127 p-type (Bi0.2Sb0.8)2Te3 and n-type Bi2(Te0.96Se0.04)3 thermoelement pairs, each having a cross-section of 1.05×1.05 mm2, and with a figure-of-merit of 1 and a heat-to-electricity conversion efficiency of ˜5%. A heat transfer model is formulated to couple conduction in the thermoelements with convection between the Al2O3 plates and the water flow in counter-flow channel configuration. The calculated open-circuit voltages are compared to those resulting from the mean temperature differences across the TEC modules computed by CFD. The investigated parameters are: hot water inlet and outlet temperatures (373 - 413 K and 323 - 363 K, respectively), stack length (300 - 1500 mm), thermoelement length (1 - 4 mm) and hot channel heights (0.2 - 2 mm). The heat transfer model is then applied to optimize a 1 kWel stack with hot water inlet at 393 K and outlet at 353 K for either maximum heat-to-electricity conversion efficiency of 2.9% or minimum size of 0.0044 m3.

Towards next generation time-domain diffuse optics devices

NASA Astrophysics Data System (ADS)

Dalla Mora, Alberto; Contini, Davide; Arridge, Simon R.; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-03-01

Diffuse Optics is growing in terms of applications ranging from e.g. oximetry, to mammography, molecular imaging, quality assessment of food and pharmaceuticals, wood optics, physics of random media. Time-domain (TD) approaches, although appealing in terms of quantitation and depth sensibility, are presently limited to large fiber-based systems, with limited number of source-detector pairs. We present a miniaturized TD source-detector probe embedding integrated laser sources and single-photon detectors. Some electronics are still external (e.g. power supply, pulse generators, timing electronics), yet full integration on-board using already proven technologies is feasible. The novel devices were successfully validated on heterogeneous phantoms showing performances comparable to large state-of-the-art TD rack-based systems. With an investigation based on simulations we provide numerical evidence that the possibility to stack many TD compact source-detector pairs in a dense, null source-detector distance arrangement could yield on the brain cortex about 1 decade higher contrast as compared to a continuous wave (CW) approach. Further, a 3-fold increase in the maximum depth (down to 6 cm) is estimated, opening accessibility to new organs such as the lung or the heart. Finally, these new technologies show the way towards compact and wearable TD probes with orders of magnitude reduction in size and cost, for a widespread use of TD devices in real life.

A directional nucleation-zipping mechanism for triple helix formation

PubMed Central

Alberti, Patrizia; Arimondo, Paola B.; Mergny, Jean-Louis; Garestier, Thérèse; Hélène, Claude; Sun, Jian-Sheng

2002-01-01

A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T·A base pair by a C·G pair at either the 5′ or the 3′ end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5′ side of the triplex (referred to as the 5′ side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5′ end to the 3′ end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5′ than at the 3′ duplex–triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression. PMID:12490709

Deformation induced microtwins and stacking faults in aluminum single crystal.

PubMed

Han, W Z; Cheng, G M; Li, S X; Wu, S D; Zhang, Z F

2008-09-12

Microtwins and stacking faults in plastically deformed aluminum single crystal were successfully observed by high-resolution transmission electron microscope. The occurrence of these microtwins and stacking faults is directly related to the specially designed crystallographic orientation, because they were not observed in pure aluminum single crystal or polycrystal before. Based on the new finding above, we propose a universal dislocation-based model to judge the preference or not for the nucleation of deformation twins and stacking faults in various face-centered-cubic metals in terms of the critical stress for dislocation glide or twinning by considering the intrinsic factors, such as stacking fault energy, crystallographic orientation, and grain size. The new finding of deformation induced microtwins and stacking faults in aluminum single crystal and the proposed model should be of interest to a broad community.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting.

PubMed

Ensslen, Philipp; Wagenknecht, Hans-Achim

2015-10-20

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

3-Chloro-4-methyl­quinolin-2(1H)-one

PubMed Central

Kassem, Mohamed G.; Ghabbour, Hazem A.; Abdel-Aziz, Hatem A.; Fun, Hoong-Kun; Ooi, Chin Wei

2012-01-01

The title compound, C10H8ClNO, is almost planar (r.m.s. deviation for the 13 non-H atoms = 0.023 Å). In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R 2 2(8) rings. Weak aromatic π–π stacking inter­actions [centroid–centroid distance = 3.7622 (12) Å] also occur. PMID:22589913

Multi-clad black display panel

DOEpatents

Veligdan, James T.; Biscardi, Cyrus; Brewster, Calvin

2002-01-01

A multi-clad black display panel, and a method of making a multi-clad black display panel, are disclosed, wherein a plurality of waveguides, each of which includes a light-transmissive core placed between an opposing pair of transparent cladding layers and a black layer disposed between transparent cladding layers, are stacked together and sawed at an angle to produce a wedge-shaped optical panel having an inlet face and an outlet face.

Disc rotors with permanent magnets for brushless DC motor

DOEpatents

Hawsey, Robert A.; Bailey, J. Milton

1992-01-01

A brushless dc permanent magnet motor drives an autonomous underwater vehe. In one embodiment, the motor comprises four substantially flat stators in stacked relationship, with pairs of the stators axially spaced, each of the stators comprising a tape-wound stator coil, and first and second substantially flat rotors disposed between the spaced pairs of stators. Each of the rotors includes an annular array of permanent magnets embedded therein. A first shaft is connected to the first rotor and a second, concentric shaft is connected to the second rotor, and a drive unit causes rotation of the two shafts in opposite directions. The second shaft comprises a hollow tube having a central bore in which the first shaft is disposed. Two different sets of bearings support the first and second shafts. In another embodiment, the motor comprises two ironless stators and pairs of rotors mounted on opposite sides of the stators and driven by counterrotating shafts.

Multispectroscopic methods reveal different modes of interaction of anti cancer drug mitoxantrone with Poly(dG-dC).Poly(dG-dC) and Poly(dA-dT).Poly(dA-dT).

PubMed

Awasthi, Pamita; Dogra, Shilpa; Barthwal, Ritu

2013-10-05

The interaction of mitoxantrone with alternating Poly(dG-dC).Poly(dG-dC) and Poly(dA-dT).Poly(dA-dT) duplex has been studied by absorption, fluorescence and Circular Dichroism (CD) spectroscopy at Drug to Phosphate base pair ratios D/P=20.0-0.04. Binding to GC polymer occurs in two distinct modes: partial stacking characterized by red shifts of 18-23nm at D/P=0.2-0.8 and external binding at D/P=1.0-20.0 whereas that to AT polymer occurs externally in the entire range of D/P. The binding constant and number of binding sites is 3.7×10(5)M(-1), 0.3 and 1.3× 10(4)M(-1), 1.5 in GC and AT polymers, respectively at low D/P ratios. CD binding isotherms show breakpoints at D/P=0.1, 0.5 and 0.25, 0.5 in GC and AT polymers, respectively. The intrinsic CD bands indicate that the distortions in GC polymer are significantly higher than that in AT polymer. Docking studies show partial insertion of mitoxantrone rings between to GC base pairs in alternating GC polymer. Side chains of mitoxantrone interact specifically with base pairs and DNA backbone. The studies are relevant to the understanding of suppression or inhibition of DNA cleavage on formation of ternary complex with topoisomerase-II enzyme and hence the anti cancer action. Copyright © 2013 Elsevier B.V. All rights reserved.

A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.

PubMed

Ketkar, Amit; Zafar, Maroof K; Banerjee, Surajit; Marquez, Victor E; Egli, Martin; Eoff, Robert L

2012-06-27

Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota

PubMed Central

Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L

2012-01-01

Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2′-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2′-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (χ), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase. PMID:22632140

Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.

PubMed

Millen, Andrea L; Churchill, Cassandra D M; Manderville, Richard A; Wetmore, Stacey D

2010-10-14

Bulky DNA addition products (adducts) formed through attack at the C8 site of guanine can adopt the syn orientation about the glycosidic bond due to changes in conformational stability or hydrogen-bonding preferences directly arising from the bulky group. Indeed, the bulky substituent may improve the stability of (non-native) Hoogsteen pairs. Therefore, such adducts often result in mutations upon DNA replication. This work examines the hydrogen-bonded pairs between the Watson-Crick and Hoogsteen faces of the ortho or para C8-phenoxyl-2'-deoxyguanosine adduct and each natural (undamaged) nucleobase with the goal to clarify the conformational preference of this type of damage, as well as provide insight into the likelihood of subsequent mutation events. B3LYP/6-311+G(2df,p)//B3LYP/6-31G(d) hydrogen-bond strengths were determined using both nucleobase and nucleoside models for adduct pairs, as well as the corresponding complexes involving natural 2'-deoxyguanosine. In addition to the magnitude of the binding strengths, the R(C1'···C1') distances and ∠(N9C1'C1') angles, as well as the degree of propeller-twist and buckle distortions, were carefully compared to the values observed in natural DNA strands. Due to structural changes in the adduct monomer upon inclusion of the sugar moiety, the monomer deformation energy significantly affects the relative hydrogen-bond strengths calculated with the nucleobase and nucleoside models. Therefore, we recommend the use of at least a nucleoside model to accurately evaluate hydrogen-bond strengths of base pairs involving flexible, bulky nucleobase adducts. Our results also emphasize the importance of considering both the magnitude of the hydrogen-bond strength and the structure of the base pair when predicting the preferential binding patterns of nucleobases. Using our best models, we conclude that the Watson-Crick face of the ortho phenoxyl adduct forms significantly more stable complexes than the Hoogsteen face, which implies that the anti orientation of the damaged base will be favored by hydrogen bonding in DNA helices. Additionally, regardless of the hydrogen-bonding face involved, cytosine forms the most stable base pair with the ortho adduct, which implies that misincorporation due to this type of damage is unlikely. Similarly, cytosine is the preferred binding partner for the Watson-Crick face of the para adduct. However, Hoogsteen interactions with the para adduct are stronger than those with natural 2'-deoxyguanosine or the ortho adduct, and this form of damage binds with nearly equal stability to both cytosine and guanine in the Hoogsteen orientation. Therefore, the para adduct may adopt multiple orientations in DNA helices and potentially cause mutations by forming pairs with different natural bases. Models of oligonucleotide duplexes must be used in future work to further evaluate other factors (stacking, major groove contacts) that may influence the conformation and binding preference of these adducts in DNA helices.

One-electron oxidation of individual DNA bases and DNA base stacks.

PubMed

Close, David M

2010-02-04

In calculations performed with DFT there is a tendency of the purine cation to be delocalized over several bases in the stack. Attempts have been made to see if methods other than DFT can be used to calculate localized cations in stacks of purines, and to relate the calculated hyperfine couplings with known experimental results. To calculate reliable hyperfine couplings it is necessary to have an adequate description of spin polarization which means that electron correlation must be treated properly. UMP2 theory has been shown to be unreliable in estimating spin densities due to overestimates of the doubles correction. Therefore attempts have been made to use quadratic configuration interaction (UQCISD) methods to treat electron correlation. Calculations on the individual DNA bases are presented to show that with UQCISD methods it is possible to calculate hyperfine couplings in good agreement with the experimental results. However these UQCISD calculations are far more time-consuming than DFT calculations. Calculations are then extended to two stacked guanine bases. Preliminary calculations with UMP2 or UQCISD theory on two stacked guanines lead to a cation localized on a single guanine base.

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

PubMed

Csaszar, K; Spacková, N; Stefl, R; Sponer, J; Leontis, N B

2001-11-09

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. The most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. To increase sampling of rare events, the native simulation was continued at 400 K. A partial, irreversible unfolding of the molecule was initiated by slippage of C8(N3+) relative to G12 and continued by sudden concerted changes in hydrogen-bonding involving A23, A24, and A25. These events were followed by a gradual loss of stacking interactions in loop 2. Of the Watson-Crick base-pairs, only the 5'-terminal pair of stem 1 dissociated at 400 K, while the trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature simulations were carried out to obtain insights into the structural and dynamic effects of selected mutations. In two of these, C8 was left unprotonated. Considerable local rearrangements occurred that were not observed in the crystal structure, thus confirming N3-protonation of C8 in the native molecule. We also investigated the effect of mutating C8(N3+) to U8, to correlate with experimental and phylogenetic studies, and of changing the G4 x C17 base-pair to A4 x U17 to weaken the trans sugar-edge interaction between positions 4 and 20 and to test models of unfolding. The simulations indicate that the C8 x G12 x C26 base-triple at the junction is the most labile region of the frame-shifting pseudoknot. They provide insights into the roles of the other non-Watson-Crick base-pairs in the early stages of unfolding of the pseudoknot, which must occur to allow readthrough of the message by the ribosome. The simulations revealed several critical, highly ordered hydration sites with close to 100 % occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50 % were also observed. Copyright 2001 Academic Press.

40 CFR 51.118 - Stack height provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... exceeds good engineering practice or by any other dispersion technique, except as provided in § 51.118(b... based on a good engineering practice stack height that exceeds the height allowed by § 51.100(ii) (1) or... actual stack height of any source. (b) The provisions of § 51.118(a) shall not apply to (1) stack heights...

Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers

NASA Astrophysics Data System (ADS)

Himbert, Sebastian; Chapman, Mindy; Deamer, David W.; Rheinstädter, Maikel C.

2016-08-01

RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5‧-adenosine monophosphate (AMP) and 5‧-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone, and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.

Monitoring the Groningen gas field by seismic noise interferometry

NASA Astrophysics Data System (ADS)

Zhou, Wen; Paulssen, Hanneke

2017-04-01

The Groningen gas field in the Netherlands is the world's 7th largest onshore gas field and has been producing from 1963. Since 2013, the year with the highest level of induced seismicity, the reservoir has been monitored by two geophone strings at reservoir level at about 3 km depth. For borehole SDM, 10 geophones with a natural frequency of 15-Hz are positioned from the top to bottom of the reservoir with a geophone spacing of 30 m. We used seismic interferometry to determine, as accurately as possible, the inter-geophone P- and S-wave velocities from ambient noise. We used 1-bit normalization and spectral whitening, together with a bandpass filter from 3 to 400 Hz. After that, for each station pair, the normalized cross-correlation was calculated for 6 seconds segments with 2/3 overlap. These segmented cross-correlations were stacked for every 1 hour, 24(hours)*33(days) segments were obtained for each station pair. The cross-correlations show both day-and-night and weekly variations reflecting fluctuations in cultural noise. The apparent P-wave travel time for each geophone pair is measured from the maximum of the vertical component cross-correlation for each of the hourly stacks. Because the distribution of these (24*33) picked travel times is not Gaussian but skewed, we used Kernel density estimations to obtain probability density functions of the travel times. The maximum likelihood travel times of all the geophone pairs was subsequently used to determine inter-geophone P-wave velocities. A good agreement was found between our estimated P velocity structure and well logging data, with difference less than 5%. The S-velocity structure was obtained from the east-component cross-correlations. They show both the direct P- and S-wave arrivals and, because of the interference, the inferred S-velocity structure is less accurate. From the 9(3x3)-component cross-correlations for all the geophone pairs, not only the direct P and S waves can be identified, but also reflected waves within the reservoir for some of the cross-correlations. It is concluded that noise interferometry can be used to determine the seismic velocity structure from deep borehole data.

Binding to the DNA Minor Groove by Heterocyclic Dications: From AT Specific Monomers to GC Recognition with Dimers

PubMed Central

Nanjunda, Rupesh; Wilson, W. David

2012-01-01

Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, they have found extensive uses in biotechnology and they are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences. PMID:23255206

Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems.

PubMed

Walsh, T R

2005-02-07

The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.

Improving ECG Classification Accuracy Using an Ensemble of Neural Network Modules

PubMed Central

Javadi, Mehrdad; Ebrahimpour, Reza; Sajedin, Atena; Faridi, Soheil; Zakernejad, Shokoufeh

2011-01-01

This paper illustrates the use of a combined neural network model based on Stacked Generalization method for classification of electrocardiogram (ECG) beats. In conventional Stacked Generalization method, the combiner learns to map the base classifiers' outputs to the target data. We claim adding the input pattern to the base classifiers' outputs helps the combiner to obtain knowledge about the input space and as the result, performs better on the same task. Experimental results support our claim that the additional knowledge according to the input space, improves the performance of the proposed method which is called Modified Stacked Generalization. In particular, for classification of 14966 ECG beats that were not previously seen during training phase, the Modified Stacked Generalization method reduced the error rate for 12.41% in comparison with the best of ten popular classifier fusion methods including Max, Min, Average, Product, Majority Voting, Borda Count, Decision Templates, Weighted Averaging based on Particle Swarm Optimization and Stacked Generalization. PMID:22046232

On-line and real-time diagnosis method for proton membrane fuel cell (PEMFC) stack by the superposition principle

NASA Astrophysics Data System (ADS)

Lee, Young-Hyun; Kim, Jonghyeon; Yoo, Seungyeol

2016-09-01

The critical cell voltage drop in a stack can be followed by stack defect. A method of detecting defective cell is the cell voltage monitoring. The other methods are based on the nonlinear frequency response. In this paper, the superposition principle for the diagnosis of PEMFC stack is introduced. If critical cell voltage drops exist, the stack behaves as a nonlinear system. This nonlinearity can explicitly appear in the ohmic overpotential region of a voltage-current curve. To detect the critical cell voltage drop, a stack is excited by two input direct test-currents which have smaller amplitude than an operating stack current and have an equal distance value from the operating current. If the difference between one voltage excited by a test current and the voltage excited by a load current is not equal to the difference between the other voltage response and the voltage excited by the load current, the stack system acts as a nonlinear system. This means that there is a critical cell voltage drop. The deviation from the value zero of the difference reflects the grade of the system nonlinearity. A simulation model for the stack diagnosis is developed based on the SPP, and experimentally validated.

A stacking method and its applications to Lanzarote tide gauge records

NASA Astrophysics Data System (ADS)

Zhu, Ping; van Ruymbeke, Michel; Cadicheanu, Nicoleta

2009-12-01

A time-period analysis tool based on stacking is introduced in this paper. The original idea comes from the classical tidal analysis method. It is assumed that the period of each major tidal component is precisely determined based on the astronomical constants and it is unchangeable with time at a given point in the Earth. We sum the tidal records at a fixed tidal component center period T then take the mean of it. The stacking could significantly increase the signal-to-noise ratio (SNR) if a certain number of stacking circles is reached. The stacking results were fitted using a sinusoidal function, the amplitude and phase of the fitting curve is computed by the least squares methods. The advantage of the method is that: (1) an individual periodical signal could be isolated by stacking; (2) one can construct a linear Stacking-Spectrum (SSP) by changing the stacking period Ts; (3) the time-period distribution of the singularity component could be approximated by a Sliding-Stacking approach. The shortcoming of the method is that in order to isolate a low energy frequency or separate the nearby frequencies, we need a long enough series with high sampling rate. The method was tested with a numeric series and then it was applied to 1788 days Lanzarote tide gauge records as an example.

A novel in situ device based on a bionic piezoelectric actuator to study tensile and fatigue properties of bulk materials.

PubMed

Wang, Shupeng; Zhang, Zhihui; Ren, Luquan; Zhao, Hongwei; Liang, Yunhong; Zhu, Bing

2014-06-01

In this work, a miniaturized device based on a bionic piezoelectric actuator was developed to investigate the static tensile and dynamic fatigue properties of bulk materials. The device mainly consists of a bionic stepping piezoelectric actuator based on wedge block clamping, a pair of grippers, and a set of precise signal test system. Tensile and fatigue examinations share a set of driving system and a set of signal test system. In situ tensile and fatigue examinations under scanning electron microscope or metallographic microscope could be carried out due to the miniaturized dimensions of the device. The structure and working principle of the device were discussed and the effects of output difference between two piezoelectric stacks on the device were theoretically analyzed. The tensile and fatigue examinations on ordinary copper were carried out using this device and its feasibility was verified through the comparison tests with a commercial tensile examination instrument.

Structural Basis of Ligand Binding by a C-di-GMP Riboswitch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, K.; Lipchock, S; Ames, T

2009-01-01

The second messenger signaling molecule bis-(3{prime}-5{prime})-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 {angstrom} resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structuralmore » data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.« less

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.

2013-10-14

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridizationmore » rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.« less

A novel in situ device based on a bionic piezoelectric actuator to study tensile and fatigue properties of bulk materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Shupeng; Zhang, Zhihui, E-mail: zhzh@jlu.edu.cn; Ren, Luquan

2014-06-15

In this work, a miniaturized device based on a bionic piezoelectric actuator was developed to investigate the static tensile and dynamic fatigue properties of bulk materials. The device mainly consists of a bionic stepping piezoelectric actuator based on wedge block clamping, a pair of grippers, and a set of precise signal test system. Tensile and fatigue examinations share a set of driving system and a set of signal test system. In situ tensile and fatigue examinations under scanning electron microscope or metallographic microscope could be carried out due to the miniaturized dimensions of the device. The structure and working principlemore » of the device were discussed and the effects of output difference between two piezoelectric stacks on the device were theoretically analyzed. The tensile and fatigue examinations on ordinary copper were carried out using this device and its feasibility was verified through the comparison tests with a commercial tensile examination instrument.« less

A putative G-quadruplex structure in the proximal promoter of vegfr-2 has implications for drug design to inhibit tumor angiogenesis.

PubMed

Liu, Yaping; Lan, Wenxian; Wang, Chunxi; Cao, Chunyang

2018-04-17

Tumor angiogenesis is mainly regulated by vascular endothelial growth factor (VEGF), produced by cancer cells. It is active on the endothelium via VEGF receptor 2 (VEGFR-2). G-quadruplexes are DNA secondary structures formed by guanine-rich sequences, for example, within gene promoters where they may contribute to transcriptional activity. The proximal promoter of vegfr-2 contains a G-quadruplex, which has been suggested to interact with small molecules that inhibit VEGFR-2 expression and thereby tumor angiogenesis. However, its structure is not known. Here, we determined its NMR solution structure, which is composed of three stacked G-tetrads containing three syn guanines. The first guanine (G1) is positioned within the central G-tetrad. We also observed that a noncanonical, V-shaped loop spans three G-tetrad planes, including no bridging nucleotides. A long and diagonal loop, which includes six nucleotides, connects reversal double chains. With a melting temperature of 54.51°C, the scaffold of this quadruplex is stabilized by one G-tetrad plane stacking with one nonstandard base pair, G3-C8, whose bases interact with each other through only one hydrogen bond. In summary, the NMR solution structure of the G-quadruplex in the proximal promoter region of the VEGFR-2 gene reported here has uncovered its key features as a potential anticancer drug target. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Modeling interactions between a β-O-4 type lignin model compound and 1-allyl-3-methylimidazolium chloride ionic liquid.

PubMed

Zhu, Youtao; Yan, Jing; Liu, Chengbu; Zhang, Dongju

2017-08-01

Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium-based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol-β-guaiacyl ether (VG) with 1-allyl-3-methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π-π stacking and intermolecular hydrogen bonding interactions. The interactions of both the cation and anion of [Amim]Cl with VG are shown to be stronger than that between the two monomers, indicating that [Amim]Cl is capable of dissolving lignin. While Cl - anion forms a hydrogen-bonded complex with VG, the imidazolium cation interacts with VG via both the π-π stacking and intermolecular hydrogen bonding. The calculated interaction energies between VG and the IL or its components (the cation, anion, and ion pair) indicate the anion plays a more important role than the cation for the dissolution of lignin in the IL. Theoretical results provide help for understanding the molecular mechanism of lignin dissolution in imidazolium-based IL. The theoretical calculations on the interaction between the lignin model compound and [Amim]Cl ionic liquid indicate that the anion of [Amim]Cl plays a more important role for lignin dissolution although the cation also makes a substantial contribution. © 2017 Wiley Periodicals, Inc.

Exploiting the potential of free software to evaluate root canal biomechanical preparation outcomes through micro-CT images.

PubMed

Neves, A A; Silva, E J; Roter, J M; Belladona, F G; Alves, H D; Lopes, R T; Paciornik, S; De-Deus, G A

2015-11-01

To propose an automated image processing routine based on free software to quantify root canal preparation outcomes in pairs of sound and instrumented roots after micro-CT scanning procedures. Seven mesial roots of human mandibular molars with different canal configuration systems were studied: (i) Vertucci's type 1, (ii) Vertucci's type 2, (iii) two individual canals, (iv) Vertucci's type 6, canals (v) with and (vi) without debris, and (vii) canal with visible pulp calcification. All teeth were instrumented with the BioRaCe system and scanned in a Skyscan 1173 micro-CT before and after canal preparation. After reconstruction, the instrumented stack of images (IS) was registered against the preoperative sound stack of images (SS). Image processing included contrast equalization and noise filtering. Sound canal volumes were obtained by a minimum threshold. For the IS, a fixed conservative threshold was chosen as the best compromise between instrumented canal and dentine whilst avoiding debris, resulting in instrumented canal plus empty spaces. Arithmetic and logical operations between sound and instrumented stacks were used to identify debris. Noninstrumented dentine was calculated using a minimum threshold in the IS and subtracting from the SS and total debris. Removed dentine volume was obtained by subtracting SS from IS. Quantitative data on total debris present in the root canal space after instrumentation, noninstrumented areas and removed dentine volume were obtained for each test case, as well as three-dimensional volume renderings. After standardization of acquisition, reconstruction and image processing micro-CT images, a quantitative approach for calculation of root canal biomechanical outcomes was achieved using free software. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Towards radiation hard converter material for SiC-based fast neutron detectors

NASA Astrophysics Data System (ADS)

Tripathi, S.; Upadhyay, C.; Nagaraj, C. P.; Venkatesan, A.; Devan, K.

2018-05-01

In the present work, Geant4 Monte-Carlo simulations have been carried out to study the neutron detection efficiency of the various neutron to other charge particle (recoil proton) converter materials. The converter material is placed over Silicon Carbide (SiC) in Fast Neutron detectors (FNDs) to achieve higher neutron detection efficiency as compared to bare SiC FNDs. Hydrogenous converter material such as High-Density Polyethylene (HDPE) is preferred over other converter materials due to the virtue of its high elastic scattering reaction cross-section for fast neutron detection at room temperature. Upon interaction with fast neutrons, hydrogenous converter material generates recoil protons which liberate e-hole pairs in the active region of SiC detector to provide a detector signal. The neutron detection efficiency offered by HDPE converter is compared with several other hydrogenous materials viz., 1) Lithium Hydride (LiH), 2) Perylene, 3) PTCDA . It is found that, HDPE, though providing highest efficiency among various studied materials, cannot withstand high temperature and harsh radiation environment. On the other hand, perylene and PTCDA can sustain harsh environments, but yields low efficiency. The analysis carried out reveals that LiH is a better material for neutron to other charge particle conversion with competent efficiency and desired radiation hardness. Further, the thickness of LiH has also been optimized for various mono-energetic neutron beams and Am-Be neutron source generating a neutron fluence of 109 neutrons/cm2. The optimized thickness of LiH converter for fast neutron detection is found to be ~ 500 μm. However, the estimated efficiency for fast neutron detection is only 0.1%, which is deemed to be inadequate for reliable detection of neutrons. A sensitivity study has also been done investigating the gamma background effect on the neutron detection efficiency for various energy threshold of Low-Level Discriminator (LLD). The detection efficiency of a stacked structure concept has been explored by juxtaposing several converter-detector layers to improve the efficiency of LiH-SiC-based FNDs . It is observed that approximately tenfold efficiency improvement has been achieved—0.93% for ten layers stacked configuration vis-à-vis 0.1% of single converter-detector layer configuration. Finally, stacked detectors have also been simulated for different converter thicknesses to attain the efficiency as high as ~ 3.25% with the help of 50 stacked layers.

Mo99 Production Plant Layout

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woloshun, Keith Albert; Dale, Gregory E.; Naranjo, Angela Carol

The NorthStar Medical Technologies 99Mo production facility configuration is envisioned to be 8 accelerator pairs irradiating 7 100Mo targets (one spare accelerator pair undergoing maintenance while the other 7 pairs are irradiating targets). The required shielding in every direction for the accelerators is initially estimated to be 10 feet of concrete. With the accelerator pairs on one (ground) level and spaced with the required shielding between adjacent pairs, the only practical path for target insertion and removal while minimizing floor space is vertical. The current scheme then requires a target vertical lift of nominally 10 feet through a shield stack.more » It is envisioned that the lift will be directly into a hot cell where an activated target can be removed from its holder and a new target attached and lowered. The hot cell is on a rail system so that a single hot cell can service all active target locations, as well as deliver the ready targets to the separations lab. On this rail system, coupled to the hot cell, will be a helium recovery and clean-up system. All helium coolant equipment is located on the upper level near to the target removal point.« less

Principles of a multistack electrochemical wastewater treatment design

NASA Astrophysics Data System (ADS)

Elsahwi, Essam S.; Dawson, Francis P.; Ruda, Harry E.

2018-02-01

Electrolyzer stacks in a bipolar architecture (cells connected in series) are desirable since power provided to a stack can be transferred at high voltages and low currents and thus the losses in the power bus can be reduced. The anode electrodes (active electrodes) considered as part of this study are single sided but there are manufacturing cost advantages to implementing double side anodes in the future. One of the main concerns with a bipolar stack implementation is the existence of leakage currents (bypass currents). The leakage current is associated with current paths that are not between adjacent anode and cathode pairs. This leads to non uniform current density distributions which compromise the electrochemical conversion efficiency of the stack and can also lead to unwanted side reactions. The objective of this paper is to develop modelling tools for a bipolar architecture consisting of two single sided cells that use single sided anodes. It is assumed that chemical reactions are single electron transfer rate limited and that diffusion and convection effects can be ignored. The design process consists of the flowing two steps: development of a large signal model for the stack, and then the extraction of a small signal model from the large signal model. The small signal model facilitates the design of a controller that satisfies current or voltage regulation requirements. A model has been developed for a single cell and two cells in series but can be generalized to more than two cells in series and to incorporate double sided anode configurations in the future. The developed model is able to determine the leakage current and thus provide a quantitative assessment on the performance of the cell.

Image registration of low signal-to-noise cryo-STEM data.

PubMed

Savitzky, Benjamin H; El Baggari, Ismail; Clement, Colin B; Waite, Emily; Goodge, Berit H; Baek, David J; Sheckelton, John P; Pasco, Christopher; Nair, Hari; Schreiber, Nathaniel J; Hoffman, Jason; Admasu, Alemayehu S; Kim, Jaewook; Cheong, Sang-Wook; Bhattacharya, Anand; Schlom, Darrell G; McQueen, Tyrel M; Hovden, Robert; Kourkoutis, Lena F

2018-08-01

Combining multiple fast image acquisitions to mitigate scan noise and drift artifacts has proven essential for picometer precision, quantitative analysis of atomic resolution scanning transmission electron microscopy (STEM) data. For very low signal-to-noise ratio (SNR) image stacks - frequently required for undistorted imaging at liquid nitrogen temperatures - image registration is particularly delicate, and standard approaches may either fail, or produce subtly specious reconstructed lattice images. We present an approach which effectively registers and averages image stacks which are challenging due to their low-SNR and propensity for unit cell misalignments. Registering all possible image pairs in a multi-image stack leads to significant information surplus. In combination with a simple physical picture of stage drift, this enables identification of incorrect image registrations, and determination of the optimal image shifts from the complete set of relative shifts. We demonstrate the effectiveness of our approach on experimental, cryogenic STEM datasets, highlighting subtle artifacts endemic to low-SNR lattice images and how they can be avoided. High-SNR average images with information transfer out to 0.72 Å are achieved at 300 kV and with the sample cooled to near liquid nitrogen temperature. Copyright © 2018 Elsevier B.V. All rights reserved.

Inverse scattering pre-stack depth imaging and it's comparison to some depth migration methods for imaging rich fault complex structure

NASA Astrophysics Data System (ADS)

Nurhandoko, Bagus Endar B.; Sukmana, Indriani; Mubarok, Syahrul; Deny, Agus; Widowati, Sri; Kurniadi, Rizal

2012-06-01

Migration is important issue for seismic imaging in complex structure. In this decade, depth imaging becomes important tools for producing accurate image in depth imaging instead of time domain imaging. The challenge of depth migration method, however, is in revealing the complex structure of subsurface. There are many methods of depth migration with their advantages and weaknesses. In this paper, we show our propose method of pre-stack depth migration based on time domain inverse scattering wave equation. Hopefully this method can be as solution for imaging complex structure in Indonesia, especially in rich thrusting fault zones. In this research, we develop a recent advance wave equation migration based on time domain inverse scattering wave which use more natural wave propagation using scattering wave. This wave equation pre-stack depth migration use time domain inverse scattering wave equation based on Helmholtz equation. To provide true amplitude recovery, an inverse of divergence procedure and recovering transmission loss are considered of pre-stack migration. Benchmarking the propose inverse scattering pre-stack depth migration with the other migration methods are also presented, i.e.: wave equation pre-stack depth migration, waveequation depth migration, and pre-stack time migration method. This inverse scattering pre-stack depth migration could image successfully the rich fault zone which consist extremely dip and resulting superior quality of seismic image. The image quality of inverse scattering migration is much better than the others migration methods.

Small stack performance of intermediate temperature-operating solid oxide fuel cells using stainless steel interconnects and anode-supported single cell

NASA Astrophysics Data System (ADS)

Bae, Joongmyeon; Lim, Sungkwang; Jee, Hyunjin; Kim, Jung Hyun; Yoo, Young-Sung; Lee, Taehee

We are developing 1 kW class solid oxide fuel cell (SOFC) system for residential power generation (RPG) application supported by Korean Government. Anode-supported single cells with thin electrolyte layer of YSZ (yttria-stabilized zirconia) or ScSZ (scandia-stabilized zirconia) for intermediate temperature operation (650-750 °C), respectively, were fabricated and small stacks were built and evaluated. The LSCF/ScSZ/Ni-YSZ single cell showed performance of 543 mW cm -2 at 650 °C and 1680 mW cm -2 at 750 °C. The voltage of 15-cell stack based on 5 cm × 5 cm single cell (LSM/YSZ/Ni-YSZ) at 150 mW was 12.5 V in hydrogen as fuel of 120 sccm per cell at 750 °C and decreased to about 10.9 V at 500 h operation time. A 5-cell stack based on the LSCF/YSZ/FL/Ni-YSZ showed the maximum power density of 30 W, 25 W and 20 W at 750 °C, 700 °C and 650 °C, respectively. LSCF/ScSZ/Ni-YSZ-based stack showed better performance than LSCF/YSZ/Ni-YSZ stack from the experiment temperature range. I- V characteristics by using hydrogen gas and reformate gas of methane as fuel were investigated at 750 °C in LSCF/ScSZ/FL/Ni-YSZ-based 5-cell stack.

Develop and test fuel cell powered on site integrated total energy sysems: Phase 3: Full-scale power plant development

NASA Technical Reports Server (NTRS)

Kaufman, A.; Olson, B.; Pudick, S.; Wang, C. L.; Werth, J.; Whelan, J. A.

1986-01-01

A 25-cell stack of the 13 inch x 23 inch cell size (about 4kW) remains on test after 8300 hours, using simulated reformate fuel. A similar stack was previously shut down after 7000 hours on load. These tests have been carried out for the purpose of assessing the durability of fuel cell stack components developed through the end of 1983. A 25kW stack containing 175 cells of the same size and utilizing a technology base representative of the 25-cell stacks has been constructed and is undergoing initial testing. A third 4kW stack is being prepared, and this stack will incorporate several new technology features.

Critical effects of alkyl chain length on fibril structures in benzene-trans(RR)- or (SS)-N,N'-alkanoyl-1,2-diaminocyclohexane gels.

PubMed

Sato, Hisako; Nakae, Takahiro; Morimoto, Kazuya; Tamura, Kenji

2012-02-28

Vibrational circular dichroism (VCD) spectra were recorded on benzene-d(6) gels formed by chiral low molecular mass gelators (LMGs), trans(RR)- or trans(SS)-N,N'-alkanoyl-1,2-diaminocyclohexane (denoted by RR-C(n) or SS-C(n), respectively; n = the number of carbon atoms in an introduced alkanoyl group). Attention was focused on the effects of alkyl chain length on the structures of the gels. When n was changed from 6 to 12, the signs of the coupled peaks around 1550 cm(-1) in the VCD spectra, which were assigned to the symmetric and asymmetric C=O stretching vibrations from the higher to lower wavenumber, respectively, critically depended on the alkyl chain length. In the case of RR-C(n), for example, the signs of the couplet were plus and minus for n = 8, 9, 10 and 12, while the signs of the same couplet were reversed for n = 6 and 7. The conformations of LMGs in fibrils were determined by comparing the observed IR and VCD spectra with those calculated for a monomeric molecule. The observed reversal of signs in the C=O couplet was rationalized in terms of the different modes of hydrogen bonding. In the case of C(8), C(9), C(10) and C(12), gelator molecules were stacked with their cyclohexyl rings in parallel, forming double anti-parallel chains of intermolecular hydrogen bonds using two pairs of >NH and >C=O groups. In case of C(6) and C(7), gelator molecules were stacked through a single chain of intermolecular hydrogen bonds using a pair of >NH and >C=O groups. The remaining pair of >NH and >C=O groups formed an intramolecular hydrogen bond.

The Direct FuelCell™ stack engineering

NASA Astrophysics Data System (ADS)

Doyon, J.; Farooque, M.; Maru, H.

FuelCell Energy (FCE) has developed power plants in the size range of 300 kW to 3 MW for distributed power generation. Field-testing of the sub-megawatt plants is underway. The FCE power plants are based on its Direct FuelCell™ (DFC) technology. This is so named because of its ability to generate electricity directly from a hydrocarbon fuel, such as natural gas, by reforming it inside the fuel cell stack itself. All FCE products use identical 8000 cm 2 cell design, approximately 350-400 cells per stack, external gas manifolds, and similar stack compression systems. The difference lies in the packaging of the stacks inside the stack module. The sub-megawatt system stack module contains a single horizontal stack whereas the MW-class stack module houses four identical vertical stacks. The commonality of the design, internal reforming features, and atmospheric operation simplify the system design, reduce cost, improve efficiency, increase reliability and maintainability. The product building-block stack design has been advanced through three full-size stack operations at company's headquarters in Danbury, CT. The initial proof-of-concept of the full-size stack design was verified in 1999, followed by a 1.5 year of endurance verification in 2000-2001, and currently a value-engineered stack version is in operation. This paper discusses the design features, important engineering solutions implemented, and test results of FCE's full-size DFC stacks.

Supramolecular architectures in two 1:1 cocrystals of 5-fluorouracil with 5-bromothiophene-2-carboxylic acid and thiophene-2-carboxylic acid.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-06-01

In solid-state engineering, cocrystallization is a strategy actively pursued for pharmaceuticals. Two 1:1 cocrystals of 5-fluorouracil (5FU; systematic name: 5-fluoro-1,3-dihydropyrimidine-2,4-dione), namely 5-fluorouracil-5-bromothiophene-2-carboxylic acid (1/1), C 5 H 3 BrO 2 S·C 4 H 3 FN 2 O 2 , (I), and 5-fluorouracil-thiophene-2-carboxylic acid (1/1), C 4 H 3 FN 2 O 2 ·C 5 H 4 O 2 S, (II), have been synthesized and characterized by single-crystal X-ray diffraction studies. In both cocrystals, carboxylic acid molecules are linked through an acid-acid R 2 2 (8) homosynthon (O-H...O) to form a carboxylic acid dimer and 5FU molecules are connected through two types of base pairs [homosynthon, R 2 2 (8) motif] via a pair of N-H...O hydrogen bonds. The crystal structures are further stabilized by C-H...O interactions in (II) and C-Br...O interactions in (I). In both crystal structures, π-π stacking and C-F...π interactions are also observed.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

PubMed Central

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

High efficiency x-ray nanofocusing by the blazed stacking of binary zone plates

NASA Astrophysics Data System (ADS)

Mohacsi, I.; Karvinen, P.; Vartiainen, I.; Diaz, A.; Somogyi, A.; Kewish, C. M.; Mercere, P.; David, C.

2013-09-01

The focusing efficiency of binary Fresnel zone plate lenses is fundamentally limited and higher efficiency requires a multi step lens profile. To overcome the manufacturing problems of high resolution and high efficiency multistep zone plates, we investigate the concept of stacking two different binary zone plates in each other's optical near-field. We use a coarse zone plate with π phase shift and a double density fine zone plate with π/2 phase shift to produce an effective 4- step profile. Using a compact experimental setup with piezo actuators for alignment, we demonstrated 47.1% focusing efficiency at 6.5 keV using a pair of 500 μm diameter and 200 nm smallest zone width. Furthermore, we present a spatially resolved characterization method using multiple diffraction orders to identify manufacturing errors, alignment errors and pattern distortions and their effect on diffraction efficiency.

Rethinking the NTCIP Design and Protocols - Analyzing the Issues

DOT National Transportation Integrated Search

1998-03-03

This working paper discusses the issues involved in changing the current draft NTCIP standard from an X.25-based protocol stack to an Internet-based protocol stack. It contains a methodology which could be used to change NTCIP's base protocols. This ...

40 CFR 51.164 - Stack height procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 51.164 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... source's stack height that exceeds good engineering practice or by any other dispersion technique, except... source based on a good engineering practice stack height that exceeds the height allowed by § 51.100(ii...

Fast concurrent array-based stacks, queues and deques using fetch-and-increment-bounded, fetch-and-decrement-bounded and store-on-twin synchronization primitives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Dong; Gara, Alana; Heidelberger, Philip

Implementation primitives for concurrent array-based stacks, queues, double-ended queues (deques) and wrapped deques are provided. In one aspect, each element of the stack, queue, deque or wrapped deque data structure has its own ticket lock, allowing multiple threads to concurrently use multiple elements of the data structure and thus achieving high performance. In another aspect, new synchronization primitives FetchAndIncrementBounded (Counter, Bound) and FetchAndDecrementBounded (Counter, Bound) are implemented. These primitives can be implemented in hardware and thus promise a very fast throughput for queues, stacks and double-ended queues.

Nitride-based stacked laser diodes with a tunnel junction

NASA Astrophysics Data System (ADS)

Okawara, Satoru; Aoki, Yuta; Kuwabara, Masakazu; Takagi, Yasufumi; Maeda, Junya; Yoshida, Harumasa

2018-01-01

We report on nitride-based two-stack laser diodes with a tunnel junction for the first time. The stacked laser diode was monolithically grown by metalorganic vapor phase epitaxy. It was confirmed that the two-stack InGaN/GaN multiple-quantum-well laser diode with an emission wavelength of 394 nm exhibited laser oscillation up to a peak output power of over 10 W in the pulsed current mode. The upper and lower emitters of the device were capable of lasing at different threshold currents of 2.4 and 5.2 A with different slope efficiencies of 0.8 and 0.3 W/A, respectively.

FPGA-Based Optical Cavity Phase Stabilization for Coherent Pulse Stacking

DOE PAGES

Xu, Yilun; Wilcox, Russell; Byrd, John; ...

2017-11-20

Coherent pulse stacking (CPS) is a new time-domain coherent addition technique that stacks several optical pulses into a single output pulse, enabling high pulse energy from fiber lasers. We develop a robust, scalable, and distributed digital control system with firmware and software integration for algorithms, to support the CPS application. We model CPS as a digital filter in the Z domain and implement a pulse-pattern-based cavity phase detection algorithm on an field-programmable gate array (FPGA). A two-stage (2+1 cavities) 15-pulse stacking system achieves an 11.0 peak-power enhancement factor. Each optical cavity is fed back at 1.5kHz, and stabilized at anmore » individually-prescribed round-trip phase with 0.7deg and 2.1deg rms phase errors for Stages 1 and 2, respectively. Optical cavity phase control with nanometer accuracy ensures 1.2% intensity stability of the stacked pulse over 12 h. The FPGA-based feedback control system can be scaled to large numbers of optical cavities.« less

On gate stack scalability of double-gate negative-capacitance FET with ferroelectric HfO2 for energy efficient sub-0.2 V operation

NASA Astrophysics Data System (ADS)

Jang, Kyungmin; Saraya, Takuya; Kobayashi, Masaharu; Hiramoto, Toshiro

2018-02-01

We have investigated the gate stack scalability and energy efficiency of double-gate negative-capacitance FET (DGNCFET) with a CMOS-compatible ferroelectric HfO2 (FE:HfO2). Analytic model-based simulation is conducted to investigate the impacts of ferroelectric characteristic of FE:HfO2 and gate stack thickness on the I on/I off ratio of DGNCFET. DGNCFET has wider design window for the gate stack where higher I on/I off ratio can be achieved than DG classical MOSFET. Under a process-induced constraint with sub-10 nm gate length (L g), FE:HfO2-based DGNCFET still has a design point for high I on/I off ratio. With an optimized gate stack thickness for sub-10 nm L g, FE:HfO2-based DGNCFET has 2.5× higher energy efficiency than DG classical MOSFET even at ultralow operation voltage of sub-0.2 V.

FPGA-Based Optical Cavity Phase Stabilization for Coherent Pulse Stacking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Yilun; Wilcox, Russell; Byrd, John

Coherent pulse stacking (CPS) is a new time-domain coherent addition technique that stacks several optical pulses into a single output pulse, enabling high pulse energy from fiber lasers. We develop a robust, scalable, and distributed digital control system with firmware and software integration for algorithms, to support the CPS application. We model CPS as a digital filter in the Z domain and implement a pulse-pattern-based cavity phase detection algorithm on an field-programmable gate array (FPGA). A two-stage (2+1 cavities) 15-pulse stacking system achieves an 11.0 peak-power enhancement factor. Each optical cavity is fed back at 1.5kHz, and stabilized at anmore » individually-prescribed round-trip phase with 0.7deg and 2.1deg rms phase errors for Stages 1 and 2, respectively. Optical cavity phase control with nanometer accuracy ensures 1.2% intensity stability of the stacked pulse over 12 h. The FPGA-based feedback control system can be scaled to large numbers of optical cavities.« less

Stacking Fault Enriching the Electronic and Transport Properties of Few-Layer Phosphorenes and Black Phosphorus.

PubMed

Lei, Shuangying; Wang, Han; Huang, Lan; Sun, Yi-Yang; Zhang, Shengbai

2016-02-10

Interface engineering is critical for enriching the electronic and transport properties of two-dimensional materials. Here, we identify a new stacking, named Aδ, in few-layer phosphorenes (FLPs) and black phosphorus (BP) based on first-principles calculation. With its low formation energy, the Aδ stacking could exist in FLPs and BP as a stacking fault. The presence of the Aδ stacking fault induces a direct to indirect transition of the band gap in FLPs. It also affects the carrier mobilities by significantly increasing the carrier effective masses. More importantly, the Aδ stacking enables the fabrication of a whole spectrum of lateral junctions with all the type-I, II, and III alignments simply through the manipulation of the van der Waals stacking without resorting to any chemical modification. This is achieved by the widely tunable electron affinity and ionization potential of FLPs and BP with the Aδ stacking.

Lowermost mantle anisotropy near the eastern edge of the Pacific LLSVP: constraints from SKS-SKKS splitting intensity measurements

NASA Astrophysics Data System (ADS)

Deng, Jie; Long, Maureen D.; Creasy, Neala; Wagner, Lara; Beck, Susan; Zandt, George; Tavera, Hernando; Minaya, Estela

2017-08-01

Seismic anisotropy has been documented in many portions of the lowermost mantle, with particularly strong anisotropy thought to be present along the edges of large low shear velocity provinces (LLSVPs). The region surrounding the Pacific LLSVP, however, has not yet been studied extensively in terms of its anisotropic structure. In this study, we use seismic data from southern Peru, northern Bolivia and Easter Island to probe lowermost mantle anisotropy beneath the eastern Pacific Ocean, mostly relying on data from the Peru Lithosphere and Slab Experiment and Central Andean Uplift and Geodynamics of High Topography experiments. Differential shear wave splitting measurements from phases that have similar ray paths in the upper mantle but different ray paths in the lowermost mantle, such as SKS and SKKS, are used to constrain anisotropy in D″. We measured splitting for 215 same station-event SKS-SKKS pairs that sample the eastern Pacific LLSVP at the base of the mantle. We used measurements of splitting intensity(SI), a measure of the amount of energy on the transverse component, to objectively and quantitatively analyse any discrepancies between SKS and SKKS phases. While the overall splitting signal is dominated by the upper-mantle anisotropy, a minority of SKS-SKKS pairs (∼10 per cent) exhibit strongly discrepant splitting between the phases (i.e. the waveforms require a difference in SI of at least 0.4), indicating a likely contribution from lowermost mantle anisotropy. In order to enhance lower mantle signals, we also stacked waveforms within individual subregions and applied a waveform differencing technique to isolate the signal from the lowermost mantle. Our stacking procedure yields evidence for substantial splitting due to lowermost mantle anisotropy only for a specific region that likely straddles the edge of Pacific LLSVP. Our observations are consistent with the localization of deformation and anisotropy near the eastern boundary of the Pacific LLSVP, similar to previous observations for the African LLSVP.

2. RICE THRESHING MILL WITH CHIMNEY STACK. Fire burned on ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. RICE THRESHING MILL WITH CHIMNEY STACK. Fire burned on top of water pipe at base of chimney stack and steam went thru pipes to boiler on south side of wall. - Mansfield Plantation, Rice Threshing Mill, U.S. Route 701 vicinity, Georgetown, Georgetown County, SC

Classifier Subset Selection for the Stacked Generalization Method Applied to Emotion Recognition in Speech

PubMed Central

Álvarez, Aitor; Sierra, Basilio; Arruti, Andoni; López-Gil, Juan-Miguel; Garay-Vitoria, Nestor

2015-01-01

In this paper, a new supervised classification paradigm, called classifier subset selection for stacked generalization (CSS stacking), is presented to deal with speech emotion recognition. The new approach consists of an improvement of a bi-level multi-classifier system known as stacking generalization by means of an integration of an estimation of distribution algorithm (EDA) in the first layer to select the optimal subset from the standard base classifiers. The good performance of the proposed new paradigm was demonstrated over different configurations and datasets. First, several CSS stacking classifiers were constructed on the RekEmozio dataset, using some specific standard base classifiers and a total of 123 spectral, quality and prosodic features computed using in-house feature extraction algorithms. These initial CSS stacking classifiers were compared to other multi-classifier systems and the employed standard classifiers built on the same set of speech features. Then, new CSS stacking classifiers were built on RekEmozio using a different set of both acoustic parameters (extended version of the Geneva Minimalistic Acoustic Parameter Set (eGeMAPS)) and standard classifiers and employing the best meta-classifier of the initial experiments. The performance of these two CSS stacking classifiers was evaluated and compared. Finally, the new paradigm was tested on the well-known Berlin Emotional Speech database. We compared the performance of single, standard stacking and CSS stacking systems using the same parametrization of the second phase. All of the classifications were performed at the categorical level, including the six primary emotions plus the neutral one. PMID:26712757

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

PubMed

Lin, C H; Patel, D J

1997-11-01

Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G.A mismatches are flanked by sheared G.A and reversed Hoogsteen G.G mismatch pairs. The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G.A mismatch formation. The recognition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

PubMed Central

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H.; Cai, Yuqin; Rodriguez, Fabian A.; Sayer, Jane M.; Jerina, Donald M.; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2012-01-01

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the non-planar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely-studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14-position with the exocyclic amino group of guanine. Here, we present the first NMR solution structure of a DB[a,l]P-derived adduct, the 14R (+)-trans-anti-DB[a,l]P–N2-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N2-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3’-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3’-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE - DNA adduct conformation differs from: (1) the classical intercalation motif where Watson-Crick base-pairing is intact at the lesion site, and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix . The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed. PMID:23121427

Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.

PubMed

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H; Cai, Yuqin; Rodriguez, Fabian A; Sayer, Jane M; Jerina, Donald M; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E

2012-12-04

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the nonplanar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14 position with the exocyclic amino group of guanine. Here, we present the first nuclear magnetic resonance solution structure of a DB[a,l]P-derived adduct, the 14R-(+)-trans-anti-DB[a,l]P-N(2)-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N(2)-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3'-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE-DNA adduct conformation differs from (1) the classical intercalation motif in which Watson-Crick base pairing is intact at the lesion site and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix. The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed.

A Thermally-Regenerative Ammonia-Based Flow Battery for Electrical Energy Recovery from Waste Heat.

PubMed

Zhu, Xiuping; Rahimi, Mohammad; Gorski, Christopher A; Logan, Bruce

2016-04-21

Large amounts of low-grade waste heat (temperatures <130 °C) are released during many industrial, geothermal, and solar-based processes. Using thermally-regenerative ammonia solutions, low-grade thermal energy can be converted to electricity in battery systems. To improve reactor efficiency, a compact, ammonia-based flow battery (AFB) was developed and tested at different solution concentrations, flow rates, cell pairs, and circuit connections. The AFB achieved a maximum power density of 45 W m(-2) (15 kW m(-3) ) and an energy density of 1260 Wh manolyte (-3) , with a thermal energy efficiency of 0.7 % (5 % relative to the Carnot efficiency). The power and energy densities of the AFB were greater than those previously reported for thermoelectrochemical and salinity-gradient technologies, and the voltage or current could be increased using stacked cells. These results demonstrated that an ammonia-based flow battery is a promising technology to convert low-grade thermal energy to electricity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Land deformation in Saint Louis, Missouri measured by ALOS InSAR and PolINSAR validated with DGPS base stations

NASA Astrophysics Data System (ADS)

Ghulam, A.

2011-12-01

DInSAR is a solid technique to estimate land subsidence and rebound using phase information from multiple SAR acquisitions over the same location from the same orbits, but from a slightly different observing geometry. However, temporal decorrelation and atmospheric effects are often a challenge to the accuracy of the DInSAR measurements. Such uncertainties may be overcome using time series interferogram stacking, e.g., permanent scatterer interferometry (Ferretti, et al., 2000, 2001). However, it requires large number of image collections. In this paper, interferometric synthetic aperture radar (InSAR) data pairs from the Phased Array type L-band Synthetic Aperture Radar (PALSAR) sensor onboard Advanced Land Observing Satellite (ALOS) are used to measure seasonal and annual land surface deformation over Saint Louis, Missouri. The datasets cover four years of time period spanning from 2006 to 2010. With the limited data coverage that is not suitable for permanent scatterer interferometry, the paper demonstrates the efficacy of dual pair interferometry from both fine-beam single polarization mode and dual-pol polarimetric images and short baseline interferometry (SBAS) approach (Berardino, et al., 2002) with an estimation accuracy comparable to differential global position systems (DGPS). We also present the impact of using assumed phase-stable ground control points versus GPS base stations for orbital refinement and phase unwrapping on overall measurement accuracy by comparing the deformation results from DInSAR and Polarimetric InSAR with DGPS base stations and ground truthing.

6. VIEW NORTHWEST OF SOUTHEAST FACADE AND STACK BASE; LOCKER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. VIEW NORTHWEST OF SOUTHEAST FACADE AND STACK BASE; LOCKER ROOM AT LEFT, COAL CONVEYOR REMAINS AT UPPER RIGHT - Turners Falls Power & Electric Company, Hampden Station, East bank of Connecticut River, Chicopee, Hampden County, MA

A stacked sequential learning method for investigator name recognition from web-based medical articles

NASA Astrophysics Data System (ADS)

Zhang, Xiaoli; Zou, Jie; Le, Daniel X.; Thoma, George

2010-01-01

"Investigator Names" is a newly required field in MEDLINE citations. It consists of personal names listed as members of corporate organizations in an article. Extracting investigator names automatically is necessary because of the increasing volume of articles reporting collaborative biomedical research in which a large number of investigators participate. In this paper, we present an SVM-based stacked sequential learning method in a novel application - recognizing named entities such as the first and last names of investigators from online medical journal articles. Stacked sequential learning is a meta-learning algorithm which can boost any base learner. It exploits contextual information by adding the predicted labels of the surrounding tokens as features. We apply this method to tag words in text paragraphs containing investigator names, and demonstrate that stacked sequential learning improves the performance of a nonsequential base learner such as an SVM classifier.

Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation.

PubMed

Banyasz, Akos; Ketola, Tiia; Martínez-Fernández, Lara; Improta, Roberto; Markovitsi, Dimitra

2018-04-17

There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

PubMed Central

Tuplin, A.; Evans, D. J.; Buckley, A.; Jones, I. M.; Gould, E. A.; Gritsun, T. S.

2011-01-01

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents. PMID:21622960

Proflavine binding to poly(rC-rA) inverts the CD spectrum but not the helix handedness.

PubMed

Westhof, E; Sundaralingam, M

1984-08-01

The interaction of proflavine hemisulfate with the sodium salt of poly(rC-rA) in solution (unbuffered) yields an inverted (mirror-like) circular dichroism (CD) spectrum to that of the free poly(rC-rA). Simultaneously, an induced negative Cotton effect appears in the proflavine band region with a maximum at 467 nm and a slight shoulder at 420 nm. This observation may be explained as resulting from the formation of a poly(rC-rA).proflavine complex with the polynucleotide existing as a right-handed parallel chain duplex with the proflavine intercalated between the CpA sequence and not the ApC sequence. The intercalation geometry here is expected to be analogous to that found in the crystal structure of the dinucleotide CpA.proflavine complex (Westhof et al. J. Mol. Biol., 1981) which forms a miniature right-handed helix. Although normally an inverted spectra could be attributed to a reversal in the helix handedness, the similarity in the 31P nuclear magnetic resonance spectra between the free and proflavine bound poly(rC-rA) indicates that their handedness is the same. The inverted CD spectrum may be a result of the different stacking orientation between the intercalated proflavine and the A-A base-pair on one hand and the triply hydrogen bonded protonated C-C base-pair on the other.

Environmentally-assisted technique for transferring devices onto non-conventional substrates

DOEpatents

Lee, Chi-Hwan; Kim, Dong Rip; Zheng, Xiaolin

2014-08-26

A device fabrication method includes: (1) providing a growth substrate including a base and an oxide layer disposed over the base; (2) forming a metal layer over the oxide layer; (3) forming a stack of device layers over the metal layer; (4) performing interfacial debonding of the metal layer to separate the stack of device layers and the metal layer from the growth substrate; and (5) affixing the stack of device layers to a target substrate.

The Stack of Yang-Mills Fields on Lorentzian Manifolds

NASA Astrophysics Data System (ADS)

Benini, Marco; Schenkel, Alexander; Schreiber, Urs

2018-03-01

We provide an abstract definition and an explicit construction of the stack of non-Abelian Yang-Mills fields on globally hyperbolic Lorentzian manifolds. We also formulate a stacky version of the Yang-Mills Cauchy problem and show that its well-posedness is equivalent to a whole family of parametrized PDE problems. Our work is based on the homotopy theoretical approach to stacks proposed in Hollander (Isr. J. Math. 163:93-124, 2008), which we shall extend by further constructions that are relevant for our purposes. In particular, we will clarify the concretification of mapping stacks to classifying stacks such as BG con.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

PubMed Central

Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-01-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

PubMed

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-02-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

Giant optical field enhancement in multi-dielectric stacks by photon scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Ndiaye, C.; Zerrad, M.; Lereu, A. L.; Roche, R.; Dumas, Ph.; Lemarchand, F.; Amra, C.

2013-09-01

Dielectric optical thin films, as opposed to metallic, have been very sparsely explored as good candidates for absorption-based optical field enhancement. In such materials, the low imaginary part of the refractive index implies that absorption processes are usually not predominant. This leads to dielectric-based optical resonances mainly via waveguiding modes. We show here that when properly designed, a multi-layered dielectric thin films stack can give rise to optical resonances linked to total absorption. We report here, on such dielectric stack designed to possess a theoretical optical field enhancement above 1000. Using photon scanning tunneling microscopy, we experimentally evaluate the resulting field enhancement of the stack as well as the associated penetration depth. We thus demonstrate the capability of multi-dielectric stacks in generating giant optical field with tunable penetration depth (down to few dozens of nm).

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd.

PubMed

Duguid, J; Bloomfield, V A; Benevides, J; Thomas, G J

1993-11-01

Interactions of divalent metal cations (Mg2+, Ca2+, Ba2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) with DNA have been investigated by laser Raman spectroscopy. Both genomic calf-thymus DNA (> 23 kilobase pairs) and mononucleosomal fragments (160 base pairs) were employed as targets of metal interaction in solutions containing 5 weight-% DNA and metal:phosphate molar ratios of 0.6:1. Raman difference spectra reveal that transition metal cations (Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) induce the greatest structural changes in B-DNA. The Raman (vibrational) band differences are extensive and indicate partial disordering of the B-form backbone, reduction in base stacking, reduction in base pairing, and specific metal interaction with acceptor sites on the purine (N7) and pyrimidine (N3) rings. Many of the observed spectral changes parallel those accompanying thermal denaturation of B-DNA and suggest that the metals link the bases of denatured DNA. While exocyclic carbonyls of dT, dG, and dC may stabilize metal ligation, correlation plots show that perturbations of the carbonyls are mainly a consequence of metal-induced denaturation of the double helix. Transition metal interactions with the DNA phosphates are weak in comparison to interactions with the bases, except in the case of Cu2+, which strongly perturbs both base and phosphate group vibrations. On the other hand, the Raman signature of B-DNA is largely unperturbed by Mg2+, Ca2+, Sr2+, and Ba2+, suggesting much weaker interactions of the alkaline earth metals with both base and phosphate sites. A notable exception is a moderate perturbation by alkaline earths of purine N7 sites in 160-base pair DNA, with Ca2+ causing the greatest effect. Correlation plots demonstrate a strong interrelationship between perturbations of Raman bands assigned to ring vibrations of the bases and those of bands assigned to exocyclic carbonyls and backbone phosphodiester groups. However, strong correlations do not occur between the Raman phosphodioxy band (centered near 1092 cm-1) and other Raman bands, suggesting that the former is not highly sensitive to the structural changes induced by divalent metal cations. The structural perturbations induced by divalent cations are much greater for > 23-kilobase pair DNA than for 160-base pair DNA, as evidenced by both the Raman difference spectra and the tendency toward the formation of insoluble aggregates. In the presence of transition metals, aggregation of high-molecular-weight DNA is evident at temperatures as low as 11 degrees C. A relationship between DNA melting and aggregation is proposed in which initial metal binding at major groove sites locally destabilizes the B-DNA double helix, causing displacement of the bases away from one another and exposing additional metal binding sites. Metal cation linkage of two displaced bases would allow separate DNA strands to crosslink. Aggregation is proposed to result from the formation of an extended network of these crosslinks.

Surface Wave Tomography of South China Sea from Ambient Seismic Noise and Two-station Measurements

NASA Astrophysics Data System (ADS)

Liang, W.-T.; Gung, Y.-C.

2012-04-01

We have taken the cross-correlation of seismic ambient noise technique as well as the two-station method to analyze the velocity structure in the South China Sea region. The dataset used in this study includes broadband waveforms recorded at the Taiwan BATS (Broadband Array in Taiwan for Seismology), Japan OHP (Ocean Hemisphere Project), Malaysia and Vietnam seismic networks. We remove the instrument response from daily data and filter the waveform with various frequency bands according to the length of each station-pair. Then we apply the commonly used 1-bit normalization to minimize the effect of earthquakes, instrumental irregularities, and non-stationary noise sources near to the stations. With the derived daily cross correlation function (CCF), we are able to examine the timing quality for each station-pair. We then obtain the surface Rayleigh wave dispersion curves from the stacked CCF for each station-pair. To cover the longer period band in the dispersion curves, we adopt the two-station method to compute both the group and phase velocities of surface waves. A new surface wave tomography based on ambient seismic noise study and traditional two-station technique has been achieved in this study. Raypaths that travel through the Central basin present higher velocity, which is in agreement with the idea of thin crust. On the other hand, the slower velocity between Taiwan and Northern Luzon, Philippine is mainly due to a thick accretionary prism above the Manila trench.

Analysis of vertical stability limits and vertical displacement event behavior on NSTX-U

NASA Astrophysics Data System (ADS)

Boyer, Mark; Battaglia, Devon; Gerhardt, Stefan; Menard, Jonathan; Mueller, Dennis; Myers, Clayton; Sabbagh, Steven; Smith, David

2017-10-01

The National Spherical Torus Experiment Upgrade (NSTX-U) completed its first run campaign in 2016, including commissioning a larger center-stack and three new tangentially aimed neutral beam sources. NSTX-U operates at increased aspect ratio due to the larger center-stack, making vertical stabilization more challenging. Since ST performance is improved at high elongation, improvements to the vertical control system were made, including use of multiple up-down-symmetric flux loop pairs for real-time estimation, and filtering to remove noise. Similar operating limits to those on NSTX (in terms of elongation and internal inductance) were achieved, now at higher aspect ratio. To better understand the observed limits and project to future operating points, a database of vertical displacement events and vertical oscillations observed during the plasma current ramp-up on NSTX/NSTX-U has been generated. Shots were clustered based on the characteristics of the VDEs/oscillations, and the plasma parameter regimes associated with the classes of behavior were studied. Results provide guidance for scenario development during ramp-up to avoid large oscillations at the time of diverting, and provide the means to assess stability of target scenarios for the next campaign. Results will also guide plans for improvements to the vertical control system. Work supported by U.S. D.O.E. Contract No. DE-AC02-09CH11466.

Develop and test fuel cell powered on-site integrated total energy systems: Phase 3, full-scale power plant development

NASA Technical Reports Server (NTRS)

Kaufman, A.; Pudick, S.; Wang, C. L.; Werth, J.; Whelan, J. A.

1985-01-01

Two 25 cell stacks of the 13 inch x 23 inch cell size (about 4kW) remain on test after 4000 hours and 2900 hours, respectively, using simulated reformate fuel. These tests are focusing on the durability of fuel cell stack components developed through the end of 1983. Also, these stacks are serving as forerunners of a 25kW stack that will contain 175 cells of the same size and will employ the same technology base. The stack technology development program has focused on a new, low cost bipolar plate edge seal technique and evaluation of advanced cathode catalysts, an electrolyte replenishment system, and nonmetallic cooling plates in small stacks.

40 CFR Appendix Vi to Part 266 - Stack Plume Rise

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 27 2011-07-01 2011-07-01 false Stack Plume Rise VI Appendix VI to Part 266 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED... FACILITIES Pt. 266, App. VI Appendix VI to Part 266—Stack Plume Rise [Estimated Plume Rise (in Meters) Based...

40 CFR Appendix Vi to Part 266 - Stack Plume Rise

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Stack Plume Rise VI Appendix VI to Part 266 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED... FACILITIES Pt. 266, App. VI Appendix VI to Part 266—Stack Plume Rise [Estimated Plume Rise (in Meters) Based...

Stacking interactions in PUF-RNA complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yiling Koh, Yvonne; Wang, Yeming; Qiu, Chen

2012-07-02

Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stackingmore » amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.« less

Correlative weighted stacking for seismic data in the wavelet domain

USGS Publications Warehouse

Zhang, S.; Xu, Y.; Xia, J.; ,

2004-01-01

Horizontal stacking plays a crucial role for modern seismic data processing, for it not only compresses random noise and multiple reflections, but also provides a foundational data for subsequent migration and inversion. However, a number of examples showed that random noise in adjacent traces exhibits correlation and coherence. The average stacking and weighted stacking based on the conventional correlative function all result in false events, which are caused by noise. Wavelet transform and high order statistics are very useful methods for modern signal processing. The multiresolution analysis in wavelet theory can decompose signal on difference scales, and high order correlative function can inhibit correlative noise, for which the conventional correlative function is of no use. Based on the theory of wavelet transform and high order statistics, high order correlative weighted stacking (HOCWS) technique is presented in this paper. Its essence is to stack common midpoint gathers after the normal moveout correction by weight that is calculated through high order correlative statistics in the wavelet domain. Synthetic examples demonstrate its advantages in improving the signal to noise (S/N) ration and compressing the correlative random noise.

A first principles approach to magnetic and optical properties in single-layer graphene sandwiched between boron nitride monolayers

NASA Astrophysics Data System (ADS)

Das, Ritwika; Chowdhury, Suman; Jana, Debnarayan

2015-07-01

The dependence of the stability of single-layer graphene (SLG) sandwiched between hexagonal boron nitride bilayers (h-BN) has been described and investigated for different types of stacking in order to provide the fingerprint of the stacking order which affects the optical properties of such trilayer systems. Considering the four stacking models AAA-, AAB-, ABA-, and ABC-type stacking, the static dielectric functions (in case of parallel polarizations) for AAB-type stacking possesses maximum values, and minimum values are noticed for AAA. However, AAA-type stacking structures contribute the maximum magnetic moment while vanishing magnetic moments are observed for ABA and ABC stacking. The observed optical anisotropy and magnetic properties of these trilayer heterostructures (h-BN/SLG/h-BN) can be understood from the crystallographic stacking order and inherent crystal lattice symmetry. These optical and magnetic results suggest that the h-BN/SLG/h-BN could provide a viable route to graphene-based opto-electronic and spintronic devices.

Charge transport in CdTe solar cells revealed by conductive tomographic atomic force microscopy

DOE PAGES

Luria, Justin; Kutes, Yasemin; Moore, Andrew; ...

2016-09-26

Polycrystalline photovoltaics comprising cadmium telluride (CdTe) represent a growing portion of the solar cell market, yet the physical picture of charge transport through the meso-scale grain morphology remains a topic of debate. It is unknown how thin film morphology affects the transport of electron-hole pairs. Accordingly this study is the first to generate three dimensional images of photocurrent throughout a thin-film solar cell, revealing the profound influence of grain boundaries and stacking faults on device efficiency.

Quantum-dot size and thin-film dielectric constant: precision measurement and disparity with simple models.

PubMed

Grinolds, Darcy D W; Brown, Patrick R; Harris, Daniel K; Bulovic, Vladimir; Bawendi, Moungi G

2015-01-14

We study the dielectric constant of lead sulfide quantum dot (QD) films as a function of the volume fraction of QDs by varying the QD size and keeping the ligand constant. We create a reliable QD sizing curve using small-angle X-ray scattering (SAXS), thin-film SAXS to extract a pair-distribution function for QD spacing, and a stacked-capacitor geometry to measure the capacitance of the thin film. Our data support a reduced dielectric constant in nanoparticles.

Fuel cell cooler assembly and edge seal means therefor

DOEpatents

Breault, Richard D.; Roethlein, Richard J.; Congdon, Joseph V.

1980-01-01

A cooler assembly for a stack of fuel cells comprises a fibrous, porous coolant tube holder sandwiched between and bonded to at least one of a pair of gas impervious graphite plates. The tubes are disposed in channels which pass through the holder. The channels are as deep as the holder thickness, which is substantially the same as the outer diameter of the tubes. Gas seals along the edges of the holder parallel to the direction of the channels are gas impervious graphite strips.

Interseismic secular deformation in Southern California from InSAR-derived maps over the time period between 1992 and 2006

NASA Astrophysics Data System (ADS)

Rivet, D. N.; Fialko, Y.

2007-12-01

We analyzed secular deformation in Southern California using an extensive catalog of InSAR data that spans 15 years between 1992 and 2006. We generated a map of the satellite line-of-sight displacements based on a stack of ~300 interferograms from 6 adjacent tracks of the ERS-1 and ERS-2 satellites covering Southern California. The main limitation to the accuracy of InSAR measurements of tectonic deformation is the atmospheric phase delay. We introduce a new method aimed to improve the signal-to-noise ratio in the InSAR- derived maps of secular deformation. The method involves identifying SAR acquisitions that are highly affected by atmospheric noise, and an optimal choice of interferometric pairs for stacking. We begin by generating a set of all possible interferometric pairs having baselines and time spans within prescribed limits. We then select interferograms with sufficiently high correlation. Subsequently, we identify noisy SAR acquisitions by means of calculating RMS of the phase signal. Finally, we generate a stack of interferograms by following a "connectivity tree" that minimizes contributions of noisy scenes. Using this method we obtained a continuous velocity field characterizing surface deformation in Southern California over the last 15 years. We identify interseismic deformation on a number of major faults, including those of the southern San Andreas system, and the Eastern California Shear Zone (ECSZ). We study the time dependency from 1992 to 2006 of those deformation patterns. Variations in the line-of- sight velocity across the Eastern California Shear Zone are non-monotonic, with the maximum along the strike of the Hector Mine fault of ~4 mm/yr, and total LOS velocity between the eastern and western boundaries of the shear zone of less than 2 mm/yr. We observe increases in the radar range to the east of ECSZ. This signal most likely results from subsidence east of the Death Valley-Mule Springs fault system, either due to hydrologic effects, or dip-slip tectonics. No resolvable interseismic deformation is detected across the Garlock fault. The Blackwater fault is associated with line-of-sight velocity of 2 mm/yr. By combining data from the ascending and descending satellite orbits, we infer that most of that strain is associated with the differential vertical motion across the fault (east side up), so that the accelerated strike-slip motion on the deep extension of the Blackwater fault is not required.

Commissioning of a conformal irradiation system for heavy-ion radiotherapy using a layer-stacking method.

PubMed

Kanai, Tatsuaki; Kanematsu, Nobuyuki; Minohara, Shinichi; Komori, Masataka; Torikoshi, Masami; Asakura, Hiroshi; Ikeda, Noritoshi; Uno, Takayuki; Takei, Yuka

2006-08-01

The commissioning of conformal radiotherapy system using heavy-ion beams at the Heavy Ion Medical Accelerator in Chiba (HIMAC) is described in detail. The system at HIMAC was upgraded for a clinical trial using a new technique: large spot uniform scanning with conformal layer stacking. The system was developed to localize the irradiation dose to the target volume more effectively than with the old system. With the present passive irradiation method using a ridge filter, a scatterer, a pair of wobbler magnets, and a multileaf collimator, the width of the spread-out Bragg peak (SOBP) in the radiation field could not be changed. With dynamic control of the beam-modifying devices during irradiation, a more conformal radiotherapy could be achieved. In order to safely perform treatments with this conformal therapy, the moving devices should be watched during irradiation and the synchronousness among the devices should be verified. This system, which has to be safe for patient irradiations, was constructed and tested for safety and for the quality of the dose localization realized. Through these commissioning tests, we were successfully able to prepare the conformal technique using layer stacking for patients. Subsequent to commissioning the technique has been applied to patients in clinical trials.

Modeling of mechanical properties of stack actuators based on electroactive polymers

NASA Astrophysics Data System (ADS)

Tepel, Dominik; Graf, Christian; Maas, Jürgen

2013-04-01

Dielectric elastomers are thin polymer films belonging to the class of electroactive polymers, which are coated with compliant and conductive electrodes on each side. Under the influence of an electrical field, dielectric elastomers perform a large amount of deformation. Depending on the mechanical setup, stack and roll actuators can be realized. In this contribution the mechanical properties of stack actuators are modeled by a holistic electromechanical approach of a single actuator film, by which the model of a stack actuator without constraints can be derived. Due to the mechanical connection between the stack actuator and the application, bulges occur at the free surfaces of the EAP material, which are calculated, experimentally validated and considered in the model of the stack actuator. Finally, the analytic actuator film model as well as the stack actuator model are validated by comparison to numerical FEM-models in ANSYS.

Visual offline sample stacking via moving neutralization boundary electrophoresis for analysis of heavy metal ion.

PubMed

Fan, Yinping; Li, Shan; Fan, Liuyin; Cao, Chengxi

2012-06-15

In this paper, a moving neutralization boundary (MNB) electrophoresis is developed as a novel model of visual offline sample stacking for the trace analysis of heavy metal ions (HMIs). In the stacking system, the cathodic-direction motion MNB is designed with 1.95-2.8mM HCl+98 mM KCl in phase alfa and 4.0mM NaOH+96 mM KCl in phase beta. If a little of HMI is present in phase alfa, the metal ion electrically migrates towards the MNB and react with hydroxyl ion, producing precipitation and moving precipitation boundary (MPB). The alkaline precipitation is neutralized by hydrogen ion, leading to a moving eluting boundary (MEB), release of HMI from its precipitation, circle of HMI from the MEB to the MPB, and highly efficient visual stacking. As a proof of concept, a set of metal ions (Cu(II), Co(II), Mn(II), Pb(II) and Cr(III)) were chosen as the model HMIs and capillary electrophoresis (CE) was selected as an analytical tool for the experiments demonstrating the feasibility of MNB-based stacking. As shown in this paper, (i) the visual stacking model was manifested by the experiments; (ii) there was a controllable stacking of HMI in the MNB system; (iii) the offline stacking could achieve higher than 123 fold preconcentration; and (iv) the five HMIs were simultaneously stacked via the developed stacking technique for the trace analyses with the limits of detection (LOD): 3.67×10(-3) (Cu(II)), 1.67×10(-3) (Co(II), 4.17×10(-3) (Mn(II)), 4.6×10(-4) (Pb(II)) and 8.40×10(-4)mM (Cr(III)). Even the off-line stacking was demonstrated for the use of CE-based HMI analysis, it has potential applications in atomic absorption spectroscopy (AAS), inductively coupled plasma-mass spectrometry (ICP-MS) and ion chromatography (IC) etc. Copyright © 2012 Elsevier B.V. All rights reserved.

A Survey of Aspartate Phenylalanine and Glutamate Phenylalanine Interactions in the Protein Data Bank: Searching for Anion Pairs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242 8249]. To study the role of anion interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused onmore » identification of Phe Asp or Glu pairs separated by less than 7 in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura Morokuma energy calculations were performed on roughly 19000 benzene formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (2 to 7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion pairs are found throughout protein structures, in helices as well as strands. Numerous pairs also had nearby cation interactions as well as potential stacking. While more than 1000 structures did not contain an anion pair, the 3134 remaining structures contained approximately 2.6 anion pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A Survey of Aspartate-Phenylalanine and Glutamate-Phenylalanine Interactions in the Protein Data Bank: Searching for Anion-pi Pairs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-{pi} pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-{pi} interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification ofmore » Phe-Asp or -Glu pairs separated by less than 7 {angstrom} in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-{pi} pairs are found throughout protein structures, in helices as well as {beta} strands. Numerous pairs also had nearby cation-{pi} interactions as well as potential {pi}-{pi} stacking. While more than 1000 structures did not contain an anion-{pi} pair, the 3134 remaining structures contained approximately 2.6 anion-{pi} pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs.

PubMed

Philip, Vivek; Harris, Jason; Adams, Rachel; Nguyen, Don; Spiers, Jeremy; Baudry, Jerome; Howell, Elizabeth E; Hinde, Robert J

2011-04-12

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.

NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus.

PubMed

D'Souza, Victoria; Dey, Anwesha; Habib, Dina; Summers, Michael F

2004-03-19

The full length, positive-strand genome of the Moloney Murine Leukemia Virus contains a "core encapsidation signal" that is essential for efficient genome packaging during virus assembly. We have determined the structure of a 101-nucleotide RNA that contains this signal (called mPsi) using a novel isotope-edited NMR approach. The method is robust and should be generally applicable to larger RNAs. mPsi folds into three stem loops, two of which (SL-C and SL-D) co-stack to form an extended helix. The third stem loop (SL-B) is connected to SL-C by a flexible, four-nucleotide linker. The structure contains five mismatched base-pairs, an unusual C.CG base-triple platform, and a novel "A-minor K-turn," in which unpaired adenosine bases A340 and A341 of a GGAA bulge pack in the minor groove of a proximal stem, and a bulged distal uridine (U319) forms a hydrogen bond with the phosphodiester of A341. Phylogenetic analyses indicate that these essential structural elements are conserved among the murine C-type retroviruses.

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

PubMed Central

Olson, W K

1975-01-01

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

Thermodynamic contributions for the incorporation of GTA triplets within canonical TAT/TAT and C+GC/C+GC base-triplet stacks of DNA triplexes.

PubMed

Soto, Ana Maria; Marky, Luis A

2002-10-15

Nucleic acid triple helices may be used in the control of gene expression. One limitation of using triplex-forming oligonucleotides as therapeutic agents is that their target sequences are limited to homopurine tracts. To increase the repertoire of sequences that can be targeted, it has been postulated that a guanine can target a thymidine forming a stable GTA mismatch triplet. In this work, we have used a combination of optical and calorimetric techniques to determine thermodynamic unfolding profiles of two triplexes containing a single GTA triplet, d(A(3)TA(3)C(5)T(3)AT(3)C(5)T(3)GT(3)) (ATA) and d(AGTGAC(5)TCACTC(5)TCGCT) (GTG), and their control triplexes, d(A(7)C(5)T(7)C(5)T(7)) (TAT7) and d(AGAGAC(5)TCTCTC(5)TCTCT) (AG5T). In general, the presence of a GTA mismatch in DNA triplexes is destabilizing; however, this destabilization is greater when placed in a C(+)GC/C(+)GC base-triplet stack than between a TAT/TAT stack. These destabilizations are accompanied by a reduced unfolding enthalpy of approximately 10 kcal/mol, suggesting a decrease in the base stacking contributions surrounding the mismatch. Relative to their corresponding control triplexes, the folding of ATA is accompanied by a lower counterion uptake and a similar proton uptake, while GTG folding is accompanied by an increase in the counterion and proton uptakes. These effects are consistent with the observed decrease in stacking interactions. The overall results indicate that the main difficulty of targeting pyrimidine interruptions is that the decrease in stacking contributions, due to the incorporation of a GTA mismatch, affects the stability of the neighboring base triplets. This suggests that nucleotide analogues that increase the strength of these base-triplet stacks will result in a more effective targeting of pyrimidine interruptions.

Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

PubMed

Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

2014-01-01

DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase

PubMed Central

Vyas, Rajan; Efthimiopoulos, Georgia; Tokarsky, E. John; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

2015-01-01

1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N2-yl)-1-aminopyrene (dG1,8), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG1,8 bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG1,8, we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG1,8 lesion in the absence or presence of dCTP. The Dpo4·DNA-dG1,8 binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4·DNA-dG1,8·dCTP ternary structure, the aminopyrene moiety of the dG1,8 lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson–Crick base pair with dG, two nucleotides upstream from the dG1,8 site, creating a complex for “-2” frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism. PMID:26327169

Systems and Methods for Fabricating Carbon Nanotube-Based Vacuum Electronic Devices

NASA Technical Reports Server (NTRS)

Manohara, Harish (Inventor); Toda, Risaku (Inventor); Del Castillo, Linda Y. (Inventor); Murthy, Rakesh (Inventor)

2015-01-01

Systems and methods in accordance with embodiments of the invention proficiently produce carbon nanotube-based vacuum electronic devices. In one embodiment a method of fabricating a carbon nanotube-based vacuum electronic device includes: growing carbon nanotubes onto a substrate to form a cathode; assembling a stack that includes the cathode, an anode, and a first layer that includes an alignment slot; disposing a microsphere partially into the alignment slot during the assembling of the stack such that the microsphere protrudes from the alignment slot and can thereby separate the first layer from an adjacent layer; and encasing the stack in a vacuum sealed container.

A novel knowledge-based potential for RNA 3D structure evaluation

NASA Astrophysics Data System (ADS)

Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

2018-03-01

Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis

PubMed Central

Ye, Fei; Zhao, Dan; Chen, Shijie; Jiang, Ren-Wang; Jiang, Hualiang; Luo, Cheng

2014-01-01

DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators. PMID:25045662

Directional charge separation in isolated organic semiconductor crystalline nanowires

DOE PAGES

Labastide, J. A.; Thompson, H. B.; Marques, S. R.; ...

2016-02-25

One of the fundamental design paradigms in organic photovoltaic device engineering is based on the idea that charge separation is an extrinsically driven process requiring an interface for exciton fission. This idea has driven an enormous materials science engineering effort focused on construction of domain sizes commensurate with a nominal exciton diffusion length of order 10 nm. Here, we show that polarized optical excitation of isolated pristine crystalline nanowires of a small molecule n-type organic semiconductor, 7,8,15,16-tetraazaterrylene, generates a significant population of charge-separated polaron pairs along the π-stacking direction. Charge separation was signalled by pronounced power-law photoluminescence decay polarized alongmore » the same axis. In the transverse direction, we observed exponential decay associated with excitons localized on individual monomers. We propose that this effect derives from an intrinsic directional charge-transfer interaction that can ultimately be programmed by molecular packing geometry.« less

Current-voltage characteristics of double stranded versus single stranded DNA molecules

NASA Astrophysics Data System (ADS)

Hartzell, B.; Chen, Hong; Heremans, J. J.; McCord, B.; Soghomonian, V.

2004-03-01

Investigation of DNA conductivity has focused on the native, duplex structure, with controversial results. Here, we present the influence of the double-helical structure on charge transport through lambda DNA molecules. The current-voltage (I-V) characteristics of both disulfide-labeled double stranded DNA (dsDNA) and disulfide-labeled single stranded DNA (ssDNA) were measured. The ssDNA was formed from the dsDNA using two different methods for comparison purposes: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics of both the double stranded and single stranded samples were close-to-linear when measured at room temperature. However, the ssDNA samples consistently gave conductivity values about two orders of magnitude smaller in amplitude. Our results suggest an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to support charge transport.(NSF NIRT 0103034)

Fabrication mechanism and photocatalytic activity for a novel graphene oxide hybrid functionalized with tetrakis-(4-hydroxylphenyl)porphyrin and 1-pyrenesulfonic acid

NASA Astrophysics Data System (ADS)

Luo, Qiang; Ge, Riyue; Kang, Shi-Zhao; Qin, Lixia; Li, Guodong; Li, Xiangqing

2018-01-01

A new type of nanohybrid (GO/THPP/PSA) was noncovalently constructed by anchoring 5, 10, 15, 20-tetrakis-(4-hydroxylphenyl)porphyrin (THPP) and 1-pyrenesulfonic acid hydrate (PSA) in graphene oxide (GO). The assembly mechanism of the nanohybrid was explored in detail. The results showed that THPP and PSA were attached in the GO by π-π stacking interaction and hydrogen bond. Compared with pure GO, GO/THPP or GO/PSA, the GO/THPP/PSA nanohybrid showed better photocatalytic activity for hydrogen evolution. The mechanism of electron transfer in the GO/THPP/PSA nanohybrid was investigated. It was shown that light absorption and separation of electron/hole pairs were improved dramatically due to wider light response and multi-channel electrons transfer in the hybrid. The results could initiate new ideas for constructing other graphene-based functionalized materials with high photocatalytic activity.

Low-Frequency Earthquakes Associated with the Late-Interseismic Central Alpine Fault, Southern Alps, New Zealand

NASA Astrophysics Data System (ADS)

Baratin, L. M.; Chamberlain, C. J.; Townend, J.; Savage, M. K.

2016-12-01

Characterising the seismicity associated with slow deformation in the vicinity of the Alpine Fault may provide constraints on the state of stress of this major transpressive margin prior to a large (≥M8) earthquake. Here, we use recently detected tremor and low-frequency earthquakes (LFEs) to examine how slow tectonic deformation is loading the Alpine Fault toward an anticipated large rupture. We initially work with a continous seismic dataset collected between 2009 and 2012 from an array of short-period seismometers, the Southern Alps Microearthquake Borehole Array. Fourteen primary LFE templates are used in an iterative matched-filter and stacking routine. This method allows the detection of similar signals and establishes LFE families with common locations. We thus generate a 36 month catalogue of 10718 LFEs. The detections are then combined for each LFE family using phase-weighted stacking to yield a signal with the highest possible signal to noise ratio. We found phase-weighted stacking to be successful in increasing the number of LFE detections by roughly 20%. Phase-weighted stacking also provides cleaner phase arrivals of apparently impulsive nature allowing more precise phase and polarity picks. We then compute improved non-linear earthquake locations using a 3D velocity model. We find LFEs to occur below the seismogenic zone at depths of 18-34 km, locating on or near the proposed deep extent of the Alpine Fault. Our next step is to estimate seismic source parameters by implementing a moment tensor inversion technique. Our focus is currently on generating a more extensive catalogue (spanning the years 2009 to 2016) using synthetic waveforms as primary templates, with which to detect LFEs. Initial testing shows that this technique paired up with phase-weighted stacking increases the number of LFE families and overall detected events roughly sevenfold. This catalogue should provide new insight into the geometry of the Alpine Fault and the prevailing stress field in the central Southern Alps.

Experimental verification of the model for formation of double Shockley stacking faults in highly doped regions of PVT-grown 4H–SiC wafers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yu; Guo, Jianqiu; Goue, Ouloide

Recently, we reported on the formation of overlapping rhombus-shaped stacking faults from scratches left over by the chemical mechanical polishing during high temperature annealing of PVT-grown 4H–SiC wafer. These stacking faults are restricted to regions with high N-doped areas of the wafer. The type of these stacking faults were determined to be Shockley stacking faults by analyzing the behavior of their area contrast using synchrotron white beam X-ray topography studies. A model was proposed to explain the formation mechanism of the rhombus shaped stacking faults based on double Shockley fault nucleation and propagation. In this paper, we have experimentally verifiedmore » this model by characterizing the configuration of the bounding partials of the stacking faults on both surfaces using synchrotron topography in back reflection geometry. As predicted by the model, on both the Si and C faces, the leading partials bounding the rhombus-shaped stacking faults are 30° Si-core and the trailing partials are 30° C-core. Finally, using high resolution transmission electron microscopy, we have verified that the enclosed stacking fault is a double Shockley type.« less

Solving the Container Stowage Problem (CSP) using Particle Swarm Optimization (PSO)

NASA Astrophysics Data System (ADS)

Matsaini; Santosa, Budi

2018-04-01

Container Stowage Problem (CSP) is a problem of containers arrangement into ships by considering rules such as: total weight, weight of one stack, destination, equilibrium, and placement of containers on vessel. Container stowage problem is combinatorial problem and hard to solve with enumeration technique. It is an NP-Hard Problem. Therefore, to find a solution, metaheuristics is preferred. The objective of solving the problem is to minimize the amount of shifting such that the unloading time is minimized. Particle Swarm Optimization (PSO) is proposed to solve the problem. The implementation of PSO is combined with some steps which are stack position change rules, stack changes based on destination, and stack changes based on the weight type of the stacks (light, medium, and heavy). The proposed method was applied on five different cases. The results were compared to Bee Swarm Optimization (BSO) and heuristics method. PSO provided mean of 0.87% gap and time gap of 60 second. While BSO provided mean of 2,98% gap and 459,6 second to the heuristcs.

Effect of pore architecture and stacking direction on mechanical properties of solid freeform fabrication-based scaffold for bone tissue engineering.

PubMed

Lee, Jung-Seob; Cha, Hwang Do; Shim, Jin-Hyung; Jung, Jin Woo; Kim, Jong Young; Cho, Dong-Woo

2012-07-01

Fabrication of a three-dimensional (3D) scaffold with increased mechanical strength may be an essential requirement for more advanced bone tissue engineering scaffolds. Various material- and chemical-based approaches have been explored to enhance the mechanical properties of engineered bone tissue scaffolds. In this study, the effects of pore architecture and stacking direction on the mechanical and cell proliferation properties of a scaffold were investigated. The 3D scaffold was prepared using solid freeform fabrication technology with a multihead deposition system. Various types of scaffolds with different pore architectures (lattice, stagger, and triangle types) and stacking directions (horizontal and vertical directions) were fabricated with a blend of polycaprolactone and poly lactic-co-glycolic acid. In compression tests, the triangle-type scaffold was the strongest among the experimental groups. Stacking direction affected the mechanical properties of scaffolds. An in vitro cell counting kit-8 assay showed no significant differences in optical density depending on the different pore architectures and stacking directions. In conclusion, mechanical properties of scaffolds can be enhanced by controlling pore architecture and stacking direction. Copyright © 2012 Wiley Periodicals, Inc.

Argos: Design and Development of Object-Oriented, Event-Driven Multimedia Data Base Technology in Support of the Paperless Ship

DTIC Science & Technology

1988-12-01

on openStack global mode -- mode may be any of the following types: -- navigate - traverse through the graphical hierarchy -- order - for...ordering an item via graphics put "NAVIGATE" into MODE hide message box hide menubar set userlevel to 5 end openStack on closestack -- this handler will... openStack hide menuBAR hide message box end openStack * BKGND #1, BUTTON #1: Next * * * * ** ** * on mouseUp visual effect wipe left go to next card of

Molecular basis for insulin fibril assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanova, Magdalena I.; Sievers, Stuart A.; Sawaya, Michael R.

2009-12-01

In the rare medical condition termed injection amyloidosis, extracellular fibrils of insulin are observed. We found that the segment of the insulin B-chain with sequence LVEALYL is the smallest segment that both nucleates and inhibits the fibrillation of full-length insulin in a molar ratio-dependent manner, suggesting that this segment is central to the cross-{beta} spine of the insulin fibril. In isolation from the rest of the protein, LVEALYL forms microcrystalline aggregates with fibrillar morphology, the structure of which we determined to 1 {angstrom} resolution. The LVEALYL segments are stacked into pairs of tightly interdigitated {beta}-sheets, each pair displaying the drymore » steric zipper interface typical of amyloid-like fibrils. This structure leads to a model for fibrils of human insulin consistent with electron microscopic, x-ray fiber diffraction, and biochemical studies.« less

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

PubMed

Sloma, Michael F; Mathews, David H

2016-12-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

3dRPC: a web server for 3D RNA-protein structure prediction.

PubMed

Huang, Yangyu; Li, Haotian; Xiao, Yi

2018-04-01

RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez Díez, Ana Luisa, E-mail: a.martinez@itma.es; Fraunhofer Institute for Solar Energy Systems ISE, Heidenhofstr. 2, 79110 Freiburg; Gutmann, Johannes

In this paper, we present a concentrator system based on a stack of fluorescent concentrators (FCs) and a bifacial solar cell. Coupling bifacial solar cells to a stack of FCs increases the performance of the system and preserves its efficiency when scaled. We used an approach to optimize a fluorescent solar concentrator system design based on a stack of multiple fluorescent concentrators (FC). Seven individual fluorescent collectors (20 mm×20 mm×2 mm) were realized by in-situ polymerization and optically characterized in regard to their ability to guide light to the edges. Then, an optimization procedure based on the experimental data ofmore » the individual FCs was carried out to determine the stack configuration that maximizes the total number of photons leaving edges. Finally, two fluorescent concentrator systems were realized by attaching bifacial silicon solar cells to the optimized FC stacks: a conventional system, where FC were attached to one side of the solar cell as a reference, and the proposed bifacial configuration. It was found that for the same overall FC area, the bifacial configuration increases the short-circuit current by a factor of 2.2, which is also in agreement with theoretical considerations.« less

Scaleable multi-format QCW pump stacks based on 200W laser diode bars and mini bars at 808nm and 940nm

NASA Astrophysics Data System (ADS)

Berk, Yuri; Karni, Yoram; Klumel, Genady; Openhaim, Yaakov; Cohen, Shalom; Yanson, Dan

2011-03-01

Advanced solid state laser architectures place increasingly demanding requirements on high-brightness, low-cost QCW laser diode pump sources, with custom apertures both for side and end rod pumping configurations. To meet this need, a new series of scaleable pump sources at 808nm and 940nm was developed. The stacks, available in multiple output formats, allow for custom aperture filling by varying both the length and quantity of stacked laser bars. For these products, we developed next-generation laser bars based on improved epitaxial wafer designs delivering power densities of 20W/mm of emission aperture. With >200W of peak QCW power available from a full-length 1cm bar, we have demonstrated power scaling to over 2kW in 10-bar stacks with 55% wall plug efficiency. We also present the design and performance of several stack configurations using full-length and reduced-length (mini) bars that demonstrate the versatility of both the bar and packaging designs. We illustrate how the ROBUST HEAD packaging technology developed at SCD is capable of accommodating variable bar length, pitch and quantity for custom rod pumping geometries. The excellent all-around performance of the stacks is supported by reliability data in line with the previously reported 20 Gshot space-grade qualification of SCD's stacks.

Raman imaging of lipid bilayer membrane by surface enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Mori, Motoaki; Abe, Shunsuke; Kondo, Takahiro; Saito, Yuika

2018-04-01

We investigated two-dimensional lipid bilayers by spectroscopic imaging with surface enhanced Raman spectroscopy (SERS). A DSPC lipid bilayer incubated on a glass substrate was coated with a thin layer of silver. Due to the strong electromagnetic enhancement of the silver film and the affinity to lipid molecules, the Raman spectrum of a single bilayer was obtained in a 1 s exposure time with 0.1 mW of incident laser power. In the C-H vibrational region of the spectra, which is sensitive to bilayer configurations, a randomly stacked area was dominated by the CH3 asymmetric-stretch mode, whereas flat areas including double bilayers showed typical SERS spectra. The spectral features of the randomly stacked area are explained by the existence of many free lipid molecules, which is supported by DFT calculations of paired DSPC molecules. Our method can be applied to reveal the local crystallinity of single lipid bilayers, which is difficult to assess by conventional Raman imaging.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhlina, Ya. A., E-mail: altik@inbox.ru; Bolotin, B. M.; Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru

Two crystal modifications (1o and 1y) of N-butyl-2-cyano-3-[4-(dimethylamino)phenyl]-2-propenamide, which differ in the color of crystals and the color of luminescence, have been studied by X-ray diffraction and spectral-luminescence methods. The corresponding bond lengths and bond angles in the molecules of two crystal modifications are virtually identical. In both crystal structures, there are two systems of weak intermolecular interactions: {pi}-stacking interactions and -CN Horizontal-Ellipsis H-N hydrogen bonds involving nitrile and NH groups. In the crystal structures, two hydrogen bonds connect pairs of molecules into centrosymmetric dimers. The N Horizontal-Ellipsis H distances are 2.21 and 2.41 A in 1o and 1y, respectively.more » The interplanar distances in the {pi}-stacked systems of 1o and 1y are 3.33 and 3.41 A, respectively. Both types of weak interactions are stronger in 1o than in 1y, which accounts for a larger shift of absorption and luminescence bands for the former compound.« less

(Acetyl­acetonato)dibromido[2,2-diphenyl­hydrazin-1-ido(1−)][2,2-diphenyl­hydrazin-1-ido(2−)]molybdenum(VI)

PubMed Central

Bustos, Carlos; Alvarez-Thon, Luis; Ibañez, Andrés; Sánchez, Christian

2011-01-01

In the title compound, [MoBr2(C12H11N2)(C12H10N2)(C5H7O2)], the MoVI atom is six-coordinated in a distorted octa­hedral geometry by two N atoms from the diphenyl­hydrazide(1−) and diphenyl­hydrazide(2−) ligands, two O atoms from a bidentate acetyl­acetonate ligand and two Br− ions. The mol­ecules form an inversion dimer via a pair of weak C—H⋯O hydrogen bonds and a π–π stacking inter­action with a centroid–centroid distance of 3.7401 (12) Å. Weak intra­molecular C—H⋯Br inter­actions and an intra­molecular π–π stacking inter­action with a centroid–centroid distance of 3.8118 (15) Å are also observed. PMID:21754584

Volume efficient sodium sulfur battery

DOEpatents

Mikkor, Mati

1980-01-01

In accordance with the teachings of this specification, a sodium sulfur battery is formed as follows. A plurality of box shaped sulfur electrodes are provided, the outer surfaces of which are defined by an electrolyte material. Each of the electrodes have length and width dimensions substantially greater than the thicknesses thereof as well as upwardly facing surface and a downwardly facing surface. An electrode structure is contained in each of the sulfur electrodes. A holding structure is provided for holding the plurality of sulfur electrodes in a stacked condition with the upwardly facing surface of one sulfur electrode in facing relationship to the downwardly facing surface of another sulfur electrode thereabove. A small thickness dimension separates each of the stacked electrodes thereby defining between each pair of sulfur electrodes a volume which receives the sodium reactant. A reservoir is provided for containing sodium. A manifold structure interconnects the volumes between the sulfur electrodes and the reservoir. A metering structure controls the flow of sodium between the reservoir and the manifold structure.

A flex-compressive-mode piezoelectric transducer for mechanical vibration/strain energy harvesting.

PubMed

Li, Xiaotian; Guo, Mingsen; Dong, Shuxiang

2011-04-01

A piezoelectric transducer for harvesting energy from ambient mechanical vibrations/strains under pressure condition was developed. The proposed transducer was made of two ring-type piezoelectric stacks, one pair of bow-shaped elastic plates, and one shaft that pre-compresses them. This transducer works in flex-compressive (F-C) mode, which is different from a conventional flex-tensional (F-T) one, to transfer a transversely applied force F into an amplified longitudinal force N pressing against the two piezo-stacks via the two bowshaped elastic plates, generating a large electric voltage output via piezoelectric effect. Our experimental results show that without an electric load, an F-C mode piezo-transducer could generate a maximum electric voltage output of up to 110 Vpp, and with an electric load of 40 κΩ, it a maximum power output of 14.6 mW under an acceleration excitation of 1 g peak-peak at the resonance frequency of 87 Hz. © 2011 IEEE

K-Partite RNA Secondary Structures

NASA Astrophysics Data System (ADS)

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ≥ 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ≤ k ≤ 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ≥ 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

Phosphoric and electric utility fuel cell technology development

NASA Astrophysics Data System (ADS)

Breault, R. D.; Briggs, T. A.; Congdon, J. V.; Demarche, T. E.; Gelting, R. L.; Goller, G. J.; Luoma, W. I.; McCloskey, M. W.; Mientek, A. P.; Obrien, J. J.

1984-01-01

The advancement of electric utility cell stack technology and reduction of cell stack cost was initiated. The cell stack has a nominal 10 ft (2) active area and operates at 120 psia/405(0)F. The program comprises six parallel phases, which culminate in a full height, 10-ft(2) stack verification test: (1) provides the information and services needed to manage the effort, including definition of the prototype commercial power plant; (2) develops the technical base for long term improvements to the cell stack; (3) develops materials and processing techniques for cell stack components incorporating the best available technology; (4) provides the design of hardware and conceptual processing layouts, and updates the power plant definition of Phase 1 to reflect the results of Phases 2 and 3; Phase 5 manufactures the hardware to verify the achievements of Phases 2 and 3, and analyzes the cost of this hardware; and Phase 6 tests the cell stacks assembled from the hardware of Phase 5 to assess the state of development.

Vibration mode analysis of the proton exchange membrane fuel cell stack

NASA Astrophysics Data System (ADS)

Liu, B.; Liu, L. F.; Wei, M. Y.; Wu, C. W.

2016-11-01

Proton exchange membrane fuel cell (PEMFC) stacks usually undergo vibration during packing, transportation, and serving time, in particular for those used in the automobiles or portable equipment. To study the stack vibration response, based on finite element method (FEM), a mode analysis is carried out in the present paper. Using this method, we can distinguish the local vibration from the stack global modes, predict the vibration responses, such as deformed shape and direction, and discuss the effects of the clamping configuration and the clamping force magnitude on vibration modes. It is found that when the total clamping force remains the same, increasing the bolt number can strengthen the stack resistance to vibration in the clamping direction, but cannot obviously strengthen stack resistance to vibration in the translations perpendicular to clamping direction and the three axis rotations. Increasing the total clamping force can increase both of the stack global mode and the bolt local mode frequencies, but will decrease the gasket local mode frequency.

Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way.

PubMed

Wang, Jia; Chen, Jingfei; Li, Jingwen; An, Liaoyuan; Wang, Yefei; Huang, Qingshan; Yao, Lishan

2018-06-01

A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone-backbone h-bonds (i→i-4 and i-3→i-7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i→i-4 and i-3→i-7 h-bonds, respectively. This cooperativity is supported by a protein α-helices h-bond survey in the pdb databank where stacking shortens the corresponding h-bond distances. © 2018 Wiley Periodicals, Inc.

Spatio-temporal filtering for determination of common mode error in regional GNSS networks

NASA Astrophysics Data System (ADS)

Bogusz, Janusz; Gruszczynski, Maciej; Figurski, Mariusz; Klos, Anna

2015-04-01

The spatial correlation between different stations for individual components in the regional GNSS networks seems to be significant. The mismodelling in satellite orbits, the Earth orientation parameters (EOP), largescale atmospheric effects or satellite antenna phase centre corrections can all cause the regionally correlated errors. This kind of GPS time series errors are referred to as common mode errors (CMEs). They are usually estimated with the regional spatial filtering, such as the "stacking". In this paper, we show the stacking approach for the set of ASG-EUPOS permanent stations, assuming that spatial distribution of the CME is uniform over the whole region of Poland (more than 600 km extent). The ASG-EUPOS is a multifunctional precise positioning system based on the reference network designed for Poland. We used a 5- year span time series (2008-2012) of daily solutions in the ITRF2008 from Bernese 5.0 processed by the Military University of Technology EPN Local Analysis Centre (MUT LAC). At the beginning of our analyses concerning spatial dependencies, the correlation coefficients between each pair of the stations in the GNSS network were calculated. This analysis shows that spatio-temporal behaviour of the GPS-derived time series is not purely random, but there is the evident uniform spatial response. In order to quantify the influence of filtering using CME, the norms L1 and L2 were determined. The values of these norms were calculated for the North, East and Up components twice: before performing the filtration and after stacking. The observed reduction of the L1 and L2 norms was up to 30% depending on the dimension of the network. However, the question how to define an optimal size of CME-analysed subnetwork remains unanswered in this research, due to the fact that our network is not extended enough.

A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition

PubMed Central

Junicke, Henrik; Hart, Jonathan R.; Kisko, Jennifer; Glebov, Oleg; Kirsch, Ilan R.; Barton, Jacqueline K.

2003-01-01

A rhodium(III) complex, rac-[Rh(bpy)2phzi]3+ (bpy, 2,2′-bipyridine; phzi, benzo[a]phenazine-5,6-quinone diimine) has been designed as a sterically demanding intercalator targeted to destabilized mismatched sites in double-helical DNA. The complex is readily synthesized by condensation of the phenazine quinone with the corresponding diammine complex. Upon photoactivation, the complex promotes direct strand scission at single-base mismatch sites within the DNA duplex. As with the parent mismatch-specific reagent, [Rh(bpy)2(chrysi)]3+ [chrysene-5,6-quinone diimine (chrysi)], mismatch selectivity depends on the helix destabilization associated with mispairing. Unlike the parent chrysi complex, the phzi analogue binds and cleaves with high affinity and efficiency. The specific binding constants for CA, CC, and CT mismatches within a 31-mer oligonucleotide duplex are 0.3, 1, and 6 × 107 M−1, respectively; site-specific photocleavage is evident at nanomolar concentrations. Moreover, the specificity, defined as the ratio in binding affinities for mispaired vs. well paired sites, is maintained. The increase in affinity is attributed to greater stability in the mismatched site associated with stacking by the heterocyclic aromatic ligand. The high-affinity complex is also applied in the differential cleavage of DNA obtained from cell lines deficient in mismatch repair vs. those proficient in mismatch repair. Agreement is found between photocleavage by the mismatch-specific probes and deficiency in mismatch repair. This mismatch-specific targeting, therefore, offers a potential strategy for new chemotherapeutic design. PMID:12610209

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

Fast principal component analysis for stacking seismic data

NASA Astrophysics Data System (ADS)

Wu, Juan; Bai, Min

2018-04-01

Stacking seismic data plays an indispensable role in many steps of the seismic data processing and imaging workflow. Optimal stacking of seismic data can help mitigate seismic noise and enhance the principal components to a great extent. Traditional average-based seismic stacking methods cannot obtain optimal performance when the ambient noise is extremely strong. We propose a principal component analysis (PCA) algorithm for stacking seismic data without being sensitive to noise level. Considering the computational bottleneck of the classic PCA algorithm in processing massive seismic data, we propose an efficient PCA algorithm to make the proposed method readily applicable for industrial applications. Two numerically designed examples and one real seismic data are used to demonstrate the performance of the presented method.

Engineering aspects and hardware verification of a volume producable solid oxide fuel cell stack design for diesel auxiliary power units

NASA Astrophysics Data System (ADS)

Stelter, Michael; Reinert, Andreas; Mai, Björn Erik; Kuznecov, Mihail

A solid oxide fuel cell (SOFC) stack module is presented that is designed for operation on diesel reformate in an auxiliary power unit (APU). The stack was designed using a top-down approach, based on a specification of an APU system that is installed on board of vehicles. The stack design is planar, modular and scalable with stamped sheet metal interconnectors. It features thin membrane electrode assemblies (MEAs), such as electrolyte supported cells (ESC) and operates at elevated temperatures around 800 °C. The stack has a low pressure drop in both the anode and the cathode to facilitate a simple system layout. An overview of the technical targets met so far is given. A stack power density of 0.2 kW l -1 has been demonstrated in a fully integrated, thermally self-sustaining APU prototype running with diesel and without an external water supply.

Nonlinear Optical Properties of Traditional and Novel Materials

NASA Astrophysics Data System (ADS)

Krupa, Sean J.

Nonlinear optical processes are an excellent candidate to provide the heralded, indistinguishable, or entangled photons necessary for development of quantum mechanics based technology which currently lack bright sources of these photons. In order to support these technologies, and others, two classes of materials: traditional and novel, were investigated via optical characterization methods with goal of gaining insight into which materials and experimental conditions yield the greatest nonlinear optical effects. Optical characterization of periodically poled lithium niobate (PPLN) helped support the development of a simple, efficient photon pair source that could be easily integrated into optical networks. Additionally, an in-situ measurement of the 2nd order nonlinear optical coefficient was developed to aid in the characterization of PPLN pair sources. Lastly, an undergraduate demonstration of quantum key distribution was constructed such that students could see the primary application for PPLN photon pair sources in an affordable, approachable demonstration. A class of novel optical materials known as 2D materials has been identified as potential replacements to the traditional nonlinear optical materials discussed in Part I. Through optical characterization of second harmonic generation (SHG) the ideal conditions for spontaneous parametric downconversion were established as well as signal thresholds for successful detection. Attempts to observe SPDC produces hints that weak generate SPDC may be present in WS2 samples however this is incredibly difficult to confirm. As growth techniques of 2D materials improve, a photonic device constructed from these materials may be possible, however it will need some mechanism e.g. stacking, a cavity, etc. to help enhance the SPDC signal.

Novel vehicle detection system based on stacked DoG kernel and AdaBoost

PubMed Central

Kang, Hyun Ho; Lee, Seo Won; You, Sung Hyun

2018-01-01

This paper proposes a novel vehicle detection system that can overcome some limitations of typical vehicle detection systems using AdaBoost-based methods. The performance of the AdaBoost-based vehicle detection system is dependent on its training data. Thus, its performance decreases when the shape of a target differs from its training data, or the pattern of a preceding vehicle is not visible in the image due to the light conditions. A stacked Difference of Gaussian (DoG)–based feature extraction algorithm is proposed to address this issue by recognizing common characteristics, such as the shadow and rear wheels beneath vehicles—of vehicles under various conditions. The common characteristics of vehicles are extracted by applying the stacked DoG shaped kernel obtained from the 3D plot of an image through a convolution method and investigating only certain regions that have a similar patterns. A new vehicle detection system is constructed by combining the novel stacked DoG feature extraction algorithm with the AdaBoost method. Experiments are provided to demonstrate the effectiveness of the proposed vehicle detection system under different conditions. PMID:29513727

Focus collimator press for a collimator for gamma ray cameras

DOE Office of Scientific and Technical Information (OSTI.GOV)

York, R.N.; York, D.L.

A focus collimator press for collimators for gamma ray cameras is described comprising a pivot arm of fixed length mounted on a travelling pivot which is movable in the plane of a spaced apart work table surface in a direction toward and away from the work table. A press plate is carried at the opposite end of the fixed length pivot arm, and is maintained in registration with the same portion of the work table for pressing engagement with each undulating radiation opaque strip as it is added to the top of a collimator stack in process by movement ofmore » the travelling pivot inward toward the work table. This enables the press plate to maintain its relative position above the collimator stack and at the same time the angle of the press plate changes, becoming less acute in relation to the work table as the travelling pivot motes inwardly toward the work table. The fixed length of the pivot arm is substantially equal to the focal point of the converging apertures formed by each pair of undulating strips stacked together. Thus, the focal point of each aperture row falls substantially on the axis of the travelling pivot, and since it moves in the plane of the work table surface the focal point of each aperture row is directed to lie in the same common plane. When one of two collimator stacks made in this way is rotated 180 degrees and the two bonded together along their respective first strips, all focal points of every aperture row lie on the central axis of the completed collimator.« less

Fatigue Analysis of Proton Exchange Membrane Fuel Cell Stacks Based on Structural Stress Distribution

NASA Astrophysics Data System (ADS)

Wu, C. W.; Liu, B.; Wei, M. Y.; Liu, L. F.

2017-05-01

Proton exchange membrane fuel cell (PEMFC) stack usually undergoes various vibrations during packing, transportation and serving time, in particular for those used in the automobiles and portable equipment. Based on the Miner fatigue damage theory, the fatigue lives of the fuel cell components are first assessed. Then the component fatigue life contours of the stack are obtained under four working conditions, i.e. the three single-axial (in X-, Y- and Z-axis separately) and multi-axial random vibrations. Accordingly, the component damage under various vibrations is evaluated. The stress distribution on the gasket and PEM will greatly affect their fatigue lives. Finally, we compare the fatigue lives of 4-bolt- and 6-bolt-clamping stacks under the same total clamping force, and find that increasing the bolt number could improve the bolt fatigue lives.

Cell module and fuel conditioner development

NASA Technical Reports Server (NTRS)

Hoover, D. Q., Jr.

1981-01-01

The design features and plans for fabrication of Stacks 564 and 800 are described. The results of the OS/IES loop testing of Stack 562, endurance testing of Stack 560 and the post test analysis of Stack 561 are reported. Progress on construction and modification of the fuel cell test facilities and the 10 kW reformer test station is described. Efforts to develop the technical data base for the fuel conditioning system included vendor contacts, packed bed heat transfer tests, development of the BOLTAR computer program, and work on the detailed design of the 10 kW reformer are described.

A cross-stacked plasmonic nanowire network for high-contrast femtosecond optical switching.

PubMed

Lin, Yuanhai; Zhang, Xinping; Fang, Xiaohui; Liang, Shuyan

2016-01-21

We report an ultrafast optical switching device constructed by stacking two layers of gold nanowires into a perpendicularly crossed network, which works at a speed faster than 280 fs with an on/off modulation depth of about 22.4%. The two stacks play different roles in enhancing consistently the optical switching performance due to their different dependence on the polarization of optical electric fields. The cross-plasmon resonance based on the interaction between the perpendicularly stacked gold nanowires and its Fano-coupling with Rayleigh anomaly is the dominant mechanism for such a high-contrast optical switching device.

Weakly Hydrated Surfaces and the Binding Interactions of Small Biological Solutes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brady, J. W.; Tavagnacco, L.; Ehrlich, L.

2012-04-01

Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.

Measurement of the energy of horizontal cosmic ray muons

NASA Astrophysics Data System (ADS)

Gettert, Michael

1993-03-01

An experiment in which the energy of cosmic ray muons is determined by measuring the electron positron pairs that they radiate off when passing through matter is described. The detector is a stack of lead converters interspersed with ionization chambers for particle detection. The chambers use as active medium the liquid tetra methyl silane (TMS). The radiated quanta initiate electromagnetic cascades in the lead and are recognized due to the characteristic shower development. The energy spectrum of horizontal muons is presented and from this the primary cosmic ray spectrum is deduced.

Leaky polarizing beam splitter with adjustable leak ratio for operation in the wavelength range of 440-690 nm.

PubMed

Cheng, L; Bartlett, C L; Erwin, J K; Mansuripur, M

1997-07-01

We discuss the optomechanical design and fabrication of a novel wideband (440-690-nm), leaky polarizing beam splitter with an adjustable leak ratio. This beam splitter is an important component of a multiwavelength dynamic testbed that we have constructed for testing optical disks. The multilayer thin-film structure of the beam splitter is essentially a stacked pair of narrow-band dielectric reflectors that have been fine tuned for optimal performance. The characteristics of the fabricated device are in good agreement with our theoretical calculations.

Weakly hydrated surfaces and the binding interactions of small biological solutes.

PubMed

Brady, John W; Tavagnacco, Letizia; Ehrlich, Laurent; Chen, Mo; Schnupf, Udo; Himmel, Michael E; Saboungi, Marie-Louise; Cesàro, Attilio

2012-04-01

Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.

N-(1-Allyl-3-chloro-4-eth-oxy-1H-indazol-5-yl)-4-methyl-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2014-06-01

In the title compound, C19H20ClN3O3S, the benzene ring is inclined to the indazole ring system by 51.23 (8)°. In the crystal, mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers which stack in columns parallel to [011]. The atoms in the allyl group are disordered over two sets of sites with an occupancy ratio of 0.624 (8):0.376 (8).

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

PubMed

Blåhed, Ida-Maria; Königsson, Helena; Ericsson, Göran; Spong, Göran

2018-01-01

Monitoring of wild animal populations is challenging, yet reliable information about population processes is important for both management and conservation efforts. Access to molecular markers, such as SNPs, enables population monitoring through genotyping of various DNA sources. We have developed 96 high quality SNP markers for individual identification of moose (Alces alces), an economically and ecologically important top-herbivore in boreal regions. Reduced representation libraries constructed from 34 moose were high-throughput de novo sequenced, generating nearly 50 million read pairs. About 50 000 stacks of aligned reads containing one or more SNPs were discovered with the Stacks pipeline. Several quality criteria were applied on the candidate SNPs to find markers informative on the individual level and well representative for the population. An empirical validation by genotyping of sequenced individuals and additional moose, resulted in the selection of a final panel of 86 high quality autosomal SNPs. Additionally, five sex-specific SNPs and five SNPs for sympatric species diagnostics are included in the panel. The genotyping error rate was 0.002 for the total panel and probability of identities were low enough to separate individuals with high confidence. Moreover, the autosomal SNPs were highly informative also for population level analyses. The potential applications of this SNP panel are thus many including investigations of population size, sex ratios, relatedness, reproductive success and population structure. Ideally, SNP-based studies could improve today's population monitoring and increase our knowledge about moose population dynamics.

Fuel rod with annular nuclear fuel pellets having same U-235 enrichment and different annulus sizes for graduated enrichment loading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mildrum, C.M.

1987-08-18

A fuel rod is described for a nuclear reactor fuel assembly, comprising: (a) a hollow cladding tube; (b) a pair of end plugs connected to and sealing the cladding tube at opposite ends thereof; (c) a plurality of fuel pellets contained on the tube and being composed of fissile material having a single enrichment the value of which is at the level of the maximum enrichment loading of the rod, the pellets having provided in a stack having one end disposed adjacent to one of the end plugs and an opposite end disposed remote from the other of the endmore » plugs; and (d) a plenum spring disposed in the tube between the other end plug and the opposite end of the pellet stack for retaining the pellets in a stack form; (e) at least some of the fuel pellets having an annular configuration and at least other of the fuel pellets having a solid configuration; (f) each of some of the annular fuel pellets having an annulus of a first size; (e) each of other of the annual fuel pellets having an annulus of a second size different from the first size, whereby graduation of axial enrichment loading is provided between the annual fuel pellets of the fuel rod.« less

Structural instabilities and wrinkles at the grain boundaries in 2-D h-BN: a first-principles analysis.

PubMed

Singh, Anjali; Waghmare, Umesh V

2014-10-21

The structure of grain boundaries (GBs) or interfaces between nano-forms of carbon determines their evolution into 3-D forms with nano-scale architecture. Here, we present a general framework for the construction of interfaces in 2-D h-BN and graphene in terms of (a) stacking faults and (b) growth faults, using first-principles density functional theoretical analysis. Such interfaces or GBs involve deviation from their ideal hexagonal lattice structure. We show that a stacking fault involves a linkage of rhombal and octagonal rings (4 : 8), and a growth fault involves a linkage of paired pentagonal and octagonal rings (5 : 5 : 8). While a growth fault is energetically more stable than a stacking fault in graphene, the polarity of B and N leads to the reversal of their relative stability in h-BN. We show that the planar structure of these interfacing grains exhibits instability with respect to buckling (out-of-plane deformation), which results in the formation of a wrinkle at the grain boundary (GB) and rippling of the structure. Our analysis leads to prediction of new types of low-energy GBs of 2-D h-BN and graphene. Our results for electronic and vibrational signatures of these interfaces and an STM image of the most stable interface will facilitate their experimental characterization, particularly of the wrinkles forming spontaneously at these interfaces.

On the base-stacking in the 5'-terminal cap structure of mRNA: a fluorescence study.

PubMed Central

Nishimura, Y; Takahashi, S; Yamamoto, T; Tsuboi, M; Hattori, M; Miura, K; Yamaguchi, K; Ohtani, S; Hata, T

1980-01-01

The fluorescence at 370 nm of the 7-methylguanosine residue (m7G) is found to be quenched when the base residue is involved in a stacking interaction with the adenosine residue in the cap structure m7G5' pppA of an eukaryotic mRNA. On the basis of the observed degree of quenching, the amounts of the stacked and unstacked forms in the cap structure have been determined at various temperatures and pH's. It has been found that at pH 6.2 effective enthalpy and entropy in the unstacked leads to stacked change are delta H degrees = 4.4 +/- 0.1 kcal/mole and delta S degrees = - 14.3 +/- 0.2 e.u., respectively. The pka value for the m7G residue is found to be 7.7 at 10 degrees C and 7.3 at 30 degrees C. The stacked structure seems to be less favourable in the deprotonated form that occurs in the higher pH solution. A similar analysis of some other cap structures indicates that the stacked form in m7G5' pppN structure is favourable if N is a purine nucleoside or a 2'-O-methylpyrimidine nucleoside but not for an unmethylated pyrimidine nucleoside. PMID:7443542

A novel application of dielectric stack actuators: a pumping micromixer

NASA Astrophysics Data System (ADS)

Solano-Arana, Susana; Klug, Florian; Mößinger, Holger; Förster-Zügel, Florentine; Schlaak, Helmut F.

2018-07-01

The fabrication of pumping micromixers as a novel application of dielectric stack actuators is proposed in this work. DEA micromixers can be valuable for medical and pharmaceutical applications, due to: firstly, the biocompatibility of the used materials (PDMS and graphite); secondly, the pumping is done with peristaltic movements, allowing only the walls of the channel to be in contact with the liquid, avoiding possible contamination from external parts; and thirdly, the low flow velocity in the micromixers required in many applications. The micromixer based on peristasltic movements will not only mix, but also pump the fluids in and out the device. The developed device is a hybrid micromixer: active, because it needs a voltage source to enhance the quality and speed of the mixing; and passive, with a similar shape to the well-known Y-type micromixers. The proposed micromixer is based on twelve stack actuators distributed in: two pumping chambers, consisting of four stack actuators in series; and a mixing chamber, made of four consecutive stack actuators with 30 layers per stack. The DEA micromixer is able to mix two solutions with a flow rate of 21.5 μl min–1 at the outlet, applying 1500 V at 10 Hz and actuating two actuators at a time.

Boosting Contextual Information for Deep Neural Network Based Voice Activity Detection

DTIC Science & Technology

2015-02-01

multi-resolution stacking (MRS), which is a stack of ensemble classifiers. Each classifier in a building block inputs the concatenation of the predictions ...a base classifier in MRS, named boosted deep neural network (bDNN). bDNN first generates multiple base predictions from different contexts of a single...frame by only one DNN and then aggregates the base predictions for a better prediction of the frame, and it is different from computationally

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

PubMed Central

Takaya, Tomohisa; Su, Charlene; de La Harpe, Kimberly; Crespo-Hernández, Carlos E.; Kohler, Bern

2008-01-01

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)4, and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution. PMID:18647840

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases.

PubMed

Takaya, Tomohisa; Su, Charlene; de La Harpe, Kimberly; Crespo-Hernández, Carlos E; Kohler, Bern

2008-07-29

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)(4), and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.

AIC-based diffraction stacking for local earthquake locations at the Sumatran Fault (Indonesia)

NASA Astrophysics Data System (ADS)

Hendriyana, Andri; Bauer, Klaus; Muksin, Umar; Weber, Michael

2018-05-01

We present a new workflow for the localization of seismic events which is based on a diffraction stacking approach. In order to address the effects from complex source radiation patterns, we suggest to compute diffraction stacking from a characteristic function (CF) instead of stacking the original waveform data. A new CF, which is called in the following mAIC (modified from Akaike Information Criterion) is proposed. We demonstrate that both P- and S-wave onsets can be detected accurately. To avoid cross-talk between P and S waves due to inaccurate velocity models, we separate the P and S waves from the mAIC function by making use of polarization attributes. Then, the final image function is represented by the largest eigenvalue as a result of the covariance analysis between P- and S-image functions. Results from synthetic experiments show that the proposed diffraction stacking provides reliable results. The workflow of the diffraction stacking method was finally applied to local earthquake data from Sumatra, Indonesia. Recordings from a temporary network of 42 stations deployed for nine months around the Tarutung pull-apart basin were analysed. The seismic event locations resulting from the diffraction stacking method align along a segment of the Sumatran Fault. A more complex distribution of seismicity is imaged within and around the Tarutung basin. Two lineaments striking N-S were found in the centre of the Tarutung basin which support independent results from structural geology.

Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering

NASA Astrophysics Data System (ADS)

Shi, Chenyang

Structure and dynamics lie at the heart of the materials science. A detailed knowledge of both subjects would be foundational in understanding the materials' properties and predicting their potential applications. However, the task becomes increasingly dicult as the particle size is reduced to the nanometer scale. For nanostructured materials their laboratory x-ray scattering patterns are overlapped and broadened, making structure determination impossible. Atomic pair distribution function technique based on either synchrotron x-ray or neutron scattering data is known as the tool of choice for probing local structures. However, to solve the "structure problem" in low-dimensional materials with PDF is still challenging. For example for 2D materials of interest in this thesis the crystallographic modeling approach often yields unphysical thermal factors along stacking direction where new chemical intuitions about their actual structures and new modeling methodology/program are needed. Beyond this, lattice dynamical investigations on nanosized particles are extremely dicult. Laboratory tools such as Raman and infra-red only probe phonons at Brillouin zone center. Although in literature there are a great number of theoretical studies of their vibrational properties based on either empirical force elds or density functional theory, various approximations made in theories make the theoretical predictions less reliable. Also, there lacks the direct experiment result to validate the theory against. In this thesis, we studied the structure and dynamics of a wide variety of technologically relevant low-dimensional materials through synchrotron based x-ray PDF and high energy resolution inelastic x-ray scattering (HERIX) techniques. By collecting PDF data and employing advanced modeling program such as DiPy-CMI, we successfully determined the atomic structures of (i) emerging Ti3C2, Nb4C3 MXenes (transition metal carbides and/or nitrides) that are promising for energy storage applications, and of (ii) zirconium phenylphosphonate ion exchange materials that are proposed to separate lanthanide ions from actinide ions in nuclear waste. Both material systems have two-dimensional layered nanocrystalline structure where we observed that the stacking of layers are not in good registry, also known as turbostratic" disorder. Consequently the signals from a single layer of atoms dominate the experimental PDF{thus building up a single slab model and simulating PDF using Debye function analysis was sucient to capture the main structural features in the measured PDF data. The information on correlation length of layers along the stacking direction, however, is contained in low-Q diraction peaks in either laboratory x-ray or synchrotron x-ray scattering patterns. On the lattice dynamics side, we rst investigated the trend of atomic bonding strength in size dependent platinum nanoparticles based on temperature dependent PDF data and measured Debye temperatures. An anomalous bond softening was observed at a particle size less than 2 nm. Since Debye model gives a simple quadratic phonon density of states (PDOS) curve, which is a simplified version of real lattice dynamics, we are motivated to measure full PDOS curves on three CdSe nanoclusters by using non-resonant inelastic x-ray scattering technique. We observed an overall blue-shift of PDOS curves with decreased sizes. Our current exemplary studies will open the door to a large number of future structural and lattice dynamical studies on a much broader range of low-dimensional material systems.

SiliPET: An ultra-high resolution design of a small animal PET scanner based on stacks of double-sided silicon strip detector

NASA Astrophysics Data System (ADS)

Di Domenico, Giovanni; Zavattini, Guido; Cesca, Nicola; Auricchio, Natalia; Andritschke, Robert; Schopper, Florian; Kanbach, Gottfried

2007-02-01

We investigated with Monte Carlo simulations, using the EGSNrcMP code, the capabilities of a small animal PET scanner based on four stacks of double-sided silicon strip detectors. Each stack consists of 40 silicon detectors with dimension of 60×60×1 mm 3 and 128 orthogonal strips on each side. Two coordinates of the interaction are given by the strips, whereas the third coordinate is given by the detector number in the stack. The stacks are arranged to form a box of 5×5×6 cm 3 with minor sides opened; the box represents the minimal FOV of the scanner. The performance parameters of the SiliPET scanner have been estimated giving a (positron range limited) spatial resolution of 0.52 mm FWHM, and an absolute sensitivity of 5.1% at the center of system. Preliminary results of a proof of principle measurement done with the MEGA advanced Compton imager using a ≈1 mm diameter 22Na source, showed a focal ray tracing FWHM of 1 mm.

Fatigue of extracted lead zirconate titanate multilayer actuators under unipolar high field electric cycling

NASA Astrophysics Data System (ADS)

Wang, Hong; Lee, Sung-Min; Wang, James L.; Lin, Hua-Tay

2014-12-01

Testing of large prototype lead zirconate titanate (PZT) stacks presents substantial technical challenges to electronic testing systems, so an alternative approach that uses subunits extracted from prototypes has been pursued. Extracted 10-layer and 20-layer plate specimens were subjected to an electric cycle test under an electric field of 3.0/0.0 kV/mm, 100 Hz to 108 cycles. The effects of measurement field level and stack size (number of PZT layers) on the fatigue responses of piezoelectric and dielectric coefficients were observed. On-line monitoring permitted examination of the fatigue response of the PZT stacks. The fatigue rate (based on on-line monitoring) and the fatigue index (based on the conductance spectrum from impedance measurement or small signal measurement) were developed to quantify the fatigue status of the PZT stacks. The controlling fatigue mechanism was analyzed against the fatigue observations. The data presented can serve as input to design optimization of PZT stacks and to operation optimization in critical applications, such as piezoelectric fuel injectors in heavy-duty diesel engines.

Fatigue of extracted lead zirconate titanate multilayer actuators under unipolar high field electric cycling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hong; Lee, Sung Min; Wang, James L.

Testing of large prototype lead zirconate titanate (PZT) stacks presents substantial technical challenges to electronic testing systems, so an alternative approach that uses subunits extracted from prototypes has been pursued. Extracted 10-layer and 20-layer plate specimens were subjected to an electric cycle test under an electric field of 3.0/0.0 kV/mm, 100 Hz to 10^8 cycles. The effects of measurement field level and stack size (number of PZT layers) on the fatigue responses of piezoelectric and dielectric coefficients were observed. On-line monitoring permitted examination of the fatigue response of the PZT stacks. The fatigue rate (based on on-line monitoring) and themore » fatigue index (based on the conductance spectrum from impedance measurement or small signal measurement) were developed to quantify the fatigue status of the PZT stacks. The controlling fatigue mechanism was analyzed against the fatigue observations. The data presented can serve as input to design optimization of PZT stacks and to operation optimization in critical applications such as piezoelectric fuel injectors in heavy-duty diesel engines.« less

Fatigue of extracted lead zirconate titanate multilayer actuators under unipolar high field electric cycling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hong, E-mail: wangh@ornl.gov; Lee, Sung-Min; Wang, James L.

Testing of large prototype lead zirconate titanate (PZT) stacks presents substantial technical challenges to electronic testing systems, so an alternative approach that uses subunits extracted from prototypes has been pursued. Extracted 10-layer and 20-layer plate specimens were subjected to an electric cycle test under an electric field of 3.0/0.0 kV/mm, 100 Hz to 10{sup 8} cycles. The effects of measurement field level and stack size (number of PZT layers) on the fatigue responses of piezoelectric and dielectric coefficients were observed. On-line monitoring permitted examination of the fatigue response of the PZT stacks. The fatigue rate (based on on-line monitoring) and the fatiguemore » index (based on the conductance spectrum from impedance measurement or small signal measurement) were developed to quantify the fatigue status of the PZT stacks. The controlling fatigue mechanism was analyzed against the fatigue observations. The data presented can serve as input to design optimization of PZT stacks and to operation optimization in critical applications, such as piezoelectric fuel injectors in heavy-duty diesel engines.« less

Fatigue of extracted lead zirconate titanate multilayer actuators under unipolar high field electric cycling

DOE PAGES

Wang, Hong; Lee, Sung Min; Wang, James L.; ...

2014-12-19

Testing of large prototype lead zirconate titanate (PZT) stacks presents substantial technical challenges to electronic testing systems, so an alternative approach that uses subunits extracted from prototypes has been pursued. Extracted 10-layer and 20-layer plate specimens were subjected to an electric cycle test under an electric field of 3.0/0.0 kV/mm, 100 Hz to 10^8 cycles. The effects of measurement field level and stack size (number of PZT layers) on the fatigue responses of piezoelectric and dielectric coefficients were observed. On-line monitoring permitted examination of the fatigue response of the PZT stacks. The fatigue rate (based on on-line monitoring) and themore » fatigue index (based on the conductance spectrum from impedance measurement or small signal measurement) were developed to quantify the fatigue status of the PZT stacks. The controlling fatigue mechanism was analyzed against the fatigue observations. The data presented can serve as input to design optimization of PZT stacks and to operation optimization in critical applications such as piezoelectric fuel injectors in heavy-duty diesel engines.« less

Prognostics of Proton Exchange Membrane Fuel Cells stack using an ensemble of constraints based connectionist networks

NASA Astrophysics Data System (ADS)

Javed, Kamran; Gouriveau, Rafael; Zerhouni, Noureddine; Hissel, Daniel

2016-08-01

Proton Exchange Membrane Fuel Cell (PEMFC) is considered the most versatile among available fuel cell technologies, which qualify for diverse applications. However, the large-scale industrial deployment of PEMFCs is limited due to their short life span and high exploitation costs. Therefore, ensuring fuel cell service for a long duration is of vital importance, which has led to Prognostics and Health Management of fuel cells. More precisely, prognostics of PEMFC is major area of focus nowadays, which aims at identifying degradation of PEMFC stack at early stages and estimating its Remaining Useful Life (RUL) for life cycle management. This paper presents a data-driven approach for prognostics of PEMFC stack using an ensemble of constraint based Summation Wavelet- Extreme Learning Machine (SW-ELM) models. This development aim at improving the robustness and applicability of prognostics of PEMFC for an online application, with limited learning data. The proposed approach is applied to real data from two different PEMFC stacks and compared with ensembles of well known connectionist algorithms. The results comparison on long-term prognostics of both PEMFC stacks validates our proposition.

Microstructural characterization of high-manganese austenitic steels with different stacking fault energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sato, Shigeo, E-mail: s.sato@imr.tohoku.ac.jp; Kwon, Eui-Pyo; Imafuku, Muneyuki

Microstructures of tensile-deformed high-manganese austenitic steels exhibiting twinning-induced plasticity were analyzed by electron backscatter diffraction pattern observation and X-ray diffraction measurement to examine the influence of differences in their stacking fault energies on twinning activity during deformation. The steel specimen with the low stacking fault energy of 15 mJ/m{sup 2} had a microstructure with a high population of mechanical twins than the steel specimen with the high stacking fault energy (25 mJ/m{sup 2}). The <111> and <100> fibers developed along the tensile axis, and mechanical twinning occurred preferentially in the <111> fiber. The Schmid factors for slip and twinning deformationsmore » can explain the origin of higher twinning activity in the <111> fiber. However, the high stacking fault energy suppresses the twinning activity even in the <111> fiber. A line profile analysis based on the X-ray diffraction data revealed the relationship between the characteristics of the deformed microstructures and the stacking fault energies of the steel specimens. Although the variation in dislocation density with the tensile deformation is not affected by the stacking fault energies, the effect of the stacking fault energies on the crystallite size refinement becomes significant with a decrease in the stacking fault energies. Moreover, the stacking fault probability, which was estimated from a peak-shift analysis of the 111 and 200 diffractions, was high for the specimen with low stacking fault energy. Regardless of the difference in the stacking fault energies of the steel specimens, the refined crystallite size has a certain correlation with the stacking fault probability, indicating that whether the deformation-induced crystallite-size refinement occurs depends directly on the stacking fault probability rather than on the stacking fault energies in the present steel specimens. - Highlights: {yields} We studied effects of stacking fault energies on deformed microstructures of steels. {yields} Correlations between texture and occurrence of mechanical twinning are discussed. {yields} Evolutions of dislocations and crystallite are analyzed by line profile analysis.« less

Novel electrical energy storage system based on reversible solid oxide cells: System design and operating conditions

NASA Astrophysics Data System (ADS)

Wendel, C. H.; Kazempoor, P.; Braun, R. J.

2015-02-01

Electrical energy storage (EES) is an important component of the future electric grid. Given that no other widely available technology meets all the EES requirements, reversible (or regenerative) solid oxide cells (ReSOCs) working in both fuel cell (power producing) and electrolysis (fuel producing) modes are envisioned as a technology capable of providing highly efficient and cost-effective EES. However, there are still many challenges and questions from cell materials development to system level operation of ReSOCs that should be addressed before widespread application. This paper presents a novel system based on ReSOCs that employ a thermal management strategy of promoting exothermic methanation within the ReSOC cell-stack to provide thermal energy for the endothermic steam/CO2 electrolysis reactions during charging mode (fuel producing). This approach also serves to enhance the energy density of the stored gases. Modeling and parametric analysis of an energy storage concept is performed using a physically based ReSOC stack model coupled with thermodynamic system component models. Results indicate that roundtrip efficiencies greater than 70% can be achieved at intermediate stack temperature (680 °C) and elevated stack pressure (20 bar). The optimal operating condition arises from a tradeoff between stack efficiency and auxiliary power requirements from balance of plant hardware.

Optical parameters of the tunable Bragg reflectors in squid.

PubMed

Ghoshal, Amitabh; Demartini, Daniel G; Eck, Elizabeth; Morse, Daniel E

2013-08-06

Cephalopods (e.g. octopus, squid and cuttlefish) dynamically tune the colour and brightness of their skin for camouflage and communication using specialized skin cells called iridocytes. We use high-resolution microspectrophotometry to investigate individual tunable Bragg structures (consisting of alternating reflectin protein-containing, high-refractive index lamellae and low-refractive index inter-lamellar spaces) in live and chemically fixed iridocytes of the California market squid, Doryteuthis opalescens. This subcellular, single-stack microspectrophotometry allows for spectral normalization, permitting use of a transfer-matrix model of Bragg reflectance to calculate all the parameters of the Bragg stack-the refractive indices, dimensions and numbers of the lamellae and inter-lamellar spaces. Results of the fitting analyses show that eight or nine pairs of low- and high-index layers typically contribute to the observed reflectivity in live cells, whereas six or seven pairs of low- and high-index layers typically contribute to the reflectivity in chemically fixed cells. The reflectin-containing, high-index lamellae of live cells have a refractive index proportional to the peak reflectivity, with an average of 1.405 ± 0.012 and a maximum around 1.44, while the reflectin-containing lamellae in fixed tissue have a refractive index of 1.413 ± 0.015 suggesting a slight increase of refractive index in the process of fixation. As expected, incremental changes in refractive index contribute to the greatest incremental changes in reflectivity for those Bragg stacks with the most layers. The excursions in dimensions required to tune the measured reflected wavelength from 675 (red) to 425 nm (blue) are a decrease from ca 150 to 80 nm for the high-index lamellae and from ca 120 to 50 nm for the low-index inter-lamellar spaces. Fixation-induced dimensional changes also are quantified, leading us to suggest that further microspectrophotometric analyses of this iridocyte system can be used as a model system to quantify the effects of various methods of tissue fixation. The microspectrophotometry technique described can be expected to provide deeper insights into the molecular and physical mechanisms governing other biophotonically active cells and structures.

Wide angle and narrow-band asymmetric absorption in visible and near-infrared regime through lossy Bragg stacks

PubMed Central

Shu, Shiwei; Zhan, Yawen; Lee, Chris; Lu, Jian; Li, Yang Yang

2016-01-01

Absorber is an important component in various optical devices. Here we report a novel type of asymmetric absorber in the visible and near-infrared spectrum which is based on lossy Bragg stacks. The lossy Bragg stacks can achieve near-perfect absorption at one side and high reflection at the other within the narrow bands (several nm) of resonance wavelengths, whereas display almost identical absorption/reflection responses for the rest of the spectrum. Meanwhile, this interesting wavelength-selective asymmetric absorption behavior persists for wide angles, does not depend on polarization, and can be ascribed to the lossy characteristics of the Bragg stacks. Moreover, interesting Fano resonance with easily tailorable peak profiles can be realized using the lossy Bragg stacks. PMID:27251768

Ultraviolet absorption spectrum of the half-filled bilayer graphene

NASA Astrophysics Data System (ADS)

Apinyan, V.; Kopeć, T. K.

2018-07-01

We consider the optical properties of the half-filled AB-stacked bilayer graphene with the excitonic pairing and condensation between the layers. Both intra and interlayer local Coulomb interaction effects have been taken into account and the role of the exact Fermi energy has been discussed in details. We have calculated the absorption coefficient, refractive index, dielectric response functions and the electron energy loss spectrum for different interlayer Coulomb interaction regimes and for different temperatures. Considering the full four-band model for the interacting AB bilayer graphene, a good agreement is achieved with other theoretical and experimental works on the subject, in particular, limiting cases of the theory. The calculations, presented here, permit to estimate accurately the effects of excitonic pairing and condensation on the optical properties of the bilayer graphene. The modifications of the plasmon excitation spectrum are discussed in details for a very large interval of the interlayer interaction parameter.

Stacked Deck: An Effective, School-Based Program for the Prevention of Problem Gambling

ERIC Educational Resources Information Center

Williams, Robert J.; Wood, Robert T.; Currie, Shawn R.

2010-01-01

School-based prevention programs are an important component of problem gambling prevention, but empirically effective programs are lacking. Stacked Deck is a set of 5-6 interactive lessons that teach about the history of gambling; the true odds and "house edge"; gambling fallacies; signs, risk factors, and causes of problem gambling; and…

Centennial-scale links between Atlantic Ocean dynamics and hydroclimate over the last 4400 years: Insights from the northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Thirumalai, K.; Quinn, T. M.; Okumura, Y.; Richey, J. N.; Partin, J. W.; Poore, R. Z.

2015-12-01

Surface circulation in the Atlantic Ocean is an important mediator of global climate and yet its variability is poorly constrained on centennial timescales. Changes in the Atlantic meridional overturning circulation (AMOC) have been implicated in late Holocene climate variability in the Western Hemisphere, although the relationship between AMOC variability and hydroclimate is uncertain due to the lack of sufficiently highly resolved proxy records. Here we present a replicated reconstruction of sea-surface temperature (SST) and salinity (SSS) from the Garrison Basin in the northern Gulf of Mexico (NGOM) spanning the last 4,400 years to better constrain past sea-surface conditions. We generated time series of paired Mg/Ca (SST proxy) and δ18O (SST and SSS proxy) variations in planktic foraminifer Globigerinoides ruber (white variety) from three multi-cores collected in 2010. Using a Monte Carlo-based technique we produce a stacked record from the three multi-cores and constrain analytical, calibration, chronological, and sampling uncertainties. We apply this technique to existing paired Mg/Ca- δ18O studies in the Gulf of Mexico and Atlantic Ocean to facilitate comparison between time-uncertain proxy reconstructions. The Garrison Basin stack exhibits large centennial-scale variability (σSST~0.6°C; δ18Osw~0.17‰) and indicates a substantially cool (0.9±0.5°C) and fresh (0.26±0.1‰) Little Ice Age (LIA; 1450-1850 A.D.), corroborating extant records from the Gulf of Mexico. Focusing on the last millennium, we analyze a suite of oceanic and terrestrial proxy records to demonstrate a centennial-scale link between salt advection in the Atlantic Ocean, a diagnostic parameter of ocean circulation, and hydroclimate in the adjacent continents. The ensuing multiproxy relationships seem to be consistent with spatial field correlations of limited salinity and rainfall instrumental/reanalysis data, which suggest that NGOM salinity varies with large-scale Atlantic Ocean circulation and continental precipitation. Our results imply significant centennial-scale variability over the late Holocene and are consistent with limited observational analysis indicating a slowdown of AMOC during the LIA.

Theoretical analysis of stack gas emission velocity measurement by optical scintillation

NASA Astrophysics Data System (ADS)

Yang, Yang; Dong, Feng-Zhong; Ni, Zhi-Bo; Pang, Tao; Zeng, Zong-Yong; Wu, Bian; Zhang, Zhi-Rong

2014-04-01

Theoretical analysis for an online measurement of the stack gas flow velocity based on the optical scintillation method with a structure of two parallel optical paths is performed. The causes of optical scintillation in a stack are first introduced. Then, the principle of flow velocity measurement and its mathematical expression based on cross correlation of the optical scintillation are presented. The field test results show that the flow velocity measured by the proposed technique in this article is consistent with the value tested by the Pitot tube. It verifies the effectiveness of this method. Finally, by use of the structure function of logarithmic light intensity fluctuations, the theoretical explanation of optical scintillation spectral characteristic in low frequency is given. The analysis of the optical scintillation spectrum provides the basis for the measurement of the stack gas flow velocity and particle concentration simultaneously.

[Effect of salts, stabilizing and destabilizing the structure of water, on the stacking association of adenosine].

PubMed

Maevskiĭ, A A; Sukhorukov, B I

1976-11-01

A spectrophotometric study, based on the concentration relationship of electron absorption spectra, of the effects of salts which stabilize and destabilize the water structure on the constant (K) of adenosine: stacking association has been carried out. A significant decrease of K was observed in NaClO4 which embodied strong destabilizing effect. Opposite effect was observed on other salts studied. According to K value the stacking-interaction of adenosine in the range of salt concentration 0 divided by 3M for different anions and cations are arranged in rows: SO4--greater than Cl- greater than ClO4-; Na+ greater than Li+greater than K+. The data obtained suggest that the effect of salts on thermostability of various oligo- and polynucleotides and on B leads to C DNA transition may be essentially concerned with the effect of both cations and anions of salts on the stacking-interaction of bases.

Dynamics-based Nondestructive Structural Monitoring Teclrniques

DTIC Science & Technology

2012-05-21

plate made from AS4/8552-2 carbon epoxy prepregs . The layup sequence: was [(0/45/90/-45)S]2 as illustrated in Figure 3.37. Each layer had the...at Penn State. Hexcel AS4/8552 unidirectional carbon/epoxy prepregs were used in the fabrication as raw materials. The prepregs were cut in pieces...with different fiber orientations and 132 stacked together following different stacking sequences. The stacked prepregs then went into a vacuum

Dynamics-based Nondestructive Structural Monitoring Techniques

DTIC Science & Technology

2012-06-21

made from AS4/8552-2 carbon epoxy prepregs . The layup sequence: was [(0/45/90/-45)S]2 as illustrated in Figure 3.37. Each layer had the thickness of...using facilities available at Penn State. Hexcel AS4/8552 unidirectional carbon/epoxy prepregs were used in the fabrication as raw materials. The... prepregs were cut in pieces with different fiber orientations and 132 stacked together following different stacking sequences. The stacked prepregs

Study on the interaction of triadimenol with calf thymus DNA by multispectroscopic methods and molecular modeling

NASA Astrophysics Data System (ADS)

Zhang, Yepeng; Zhang, Guowen; Fu, Peng; Ma, Yadi; Zhou, Jia

2012-10-01

The binding mechanism of triadimenol (NOL) to calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD), Fourier transform infrared (FT-IR), and nuclear magnetic resonance (1H NMR) spectroscopy, coupled with viscosity measurements and atomic force microscopy (AFM) technique. The results suggested that NOL interacted with ctDNA by intercalation mode. CD and AFM assays showed that NOL can damage the base stacking of ctDNA and result in regional cleavage of the two DNA strands. FT-IR and 1H NMR spectra coupled with molecular docking revealed that a specific binding mainly exists between NOL and G-C base pairs of the ctDNA where two hydrogen bonds form. Moreover, the association constants of NOL with DNA at three different temperatures were determined to be in the 103 L mol-1 range. The calculated thermodynamic parameters suggested that the binding of NOL to ctDNA was driven mainly by hydrogen bond and van der Waals.

An uracil-linked hydroxyflavone probe for the recognition of ATP

PubMed Central

Bojtár, Márton; Janzsó-Berend, Péter Zoltán; Mester, Dávid; Hessz, Dóra; Kállay, Mihály; Kubinyi, Miklós

2018-01-01

Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy. Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. PMID:29719572

Spectroscopic signatures of AA' and AB stacking of chemical vapor deposited bilayer MoS 2

DOE PAGES

Xia, Ming; Li, Bo; Yin, Kuibo; ...

2015-11-04

We discuss prominent resonance Raman and photoluminescence spectroscopic differences between AA'and AB stacked bilayer molybdenum disulfide (MoS 2) grown by chemical vapor deposition are reported. Bilayer MoS 2 islands consisting of the two stacking orders were obtained under identical growth conditions. Also, resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS 2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom.

1-[(Anthracen-9-yl)carbon­yl]-2,7-di­meth­oxy­naphthalene: a chain-like structure composed of face-to-face type dimeric mol­ecular aggregates

PubMed Central

Siqingaowa; Tsumuki, Takehiro; Ogata, Kazuki; Yonezawa, Noriyuki; Okamoto, Akiko

2016-01-01

The asymmetric unit of the title compound, C27H20O3, contains two independent mol­ecules (A and B). The anthracene ring system is connected to the 2,7-di­meth­oxy­naphthalene core in a twisted manner, with dihedral angles of 86.38 (5) and 79.36 (8)°, respectively, for conformers A and B. In the crystal, face-to-face type dimeric mol­ecular aggregates of each conformer are observed. The dimer of conformer A is formed by two pairs of C—H⋯π inter­actions, and that of conformer B by a pair of (sp 2)C—H⋯O hydrogen bonds. The dimers of conformer A are linked to each other via a π–π stacking inter­action between the anthracene rings to form a chain along the b axis and the chains are aligned along the c axis, forming a sheet structure. The dimers of conformer B are connected to each other via a couple of C—H⋯π inter­actions to form a chain along the b axis. The chains are aligned along the c axis through (sp 2)C—H⋯O=C hydrogen bonds, forming a sheet parallel to the bc plane. The sheets of conformers A and B are alternately stacked along the a axis via two kinds of inter­molecular (sp 2)C—H⋯O=C hydrogen bonds. PMID:27980839

Phase-resolved and time-averaged puff motions of an excited stack-issued transverse jet

NASA Astrophysics Data System (ADS)

Hsu, C. M.; Huang, R. F.

2013-07-01

The dynamics of puff motions in an excited stack-issued transverse jet were studied experimentally in a wind tunnel. The temporal and spatial evolution processes of the puffs induced by acoustic excitation were examined using the smoke flow visualization method and high-speed particle image velocimetry. The temporal and spatial evolutions of the puffs were examined using phase-resolved ensemble-averaged velocity fields and the velocity, length scales, and vorticity characteristics of the puffs were studied. The time-averaged velocity fields were calculated to analyze the velocity distributions and vorticity contours. The results show that a puff consists of a pair of counter-rotating vortex rings. An initial vortex ring was formed due to a concentration of vorticity at the lee side of the issuing jet at the instant of the mid-oscillation cycle. A vortex ring rotating in the opposite direction to that of the initial vortex ring was subsequently formed at the upwind side of the issuing jet. These two counter-rotating vortex rings formed a "mushroom" vortex pair, which was deflected by the crossflow and traveled downstream along a time-averaged trajectory of zero vorticity. The trajectory was situated far above the time-averaged streamline evolving from the leading edge of the tube. The velocity magnitudes of the vortex rings at the upwind and the lee side decreased with time evolution as the puffs traveled downstream due to momentum dissipation and entrainment effects. The puffs traveling along the trajectory of zero vorticity caused large velocities to appear above the leading-edge streamline.

Two stage bioethanol refining with multi litre stacked microbial fuel cell and microbial electrolysis cell.

PubMed

Sugnaux, Marc; Happe, Manuel; Cachelin, Christian Pierre; Gloriod, Olivier; Huguenin, Gérald; Blatter, Maxime; Fischer, Fabian

2016-12-01

Ethanol, electricity, hydrogen and methane were produced in a two stage bioethanol refinery setup based on a 10L microbial fuel cell (MFC) and a 33L microbial electrolysis cell (MEC). The MFC was a triple stack for ethanol and electricity co-generation. The stack configuration produced more ethanol with faster glucose consumption the higher the stack potential. Under electrolytic conditions ethanol productivity outperformed standard conditions and reached 96.3% of the theoretically best case. At lower external loads currents and working potentials oscillated in a self-synchronized manner over all three MFC units in the stack. In the second refining stage, fermentation waste was converted into methane, using the scale up MEC stack. The bioelectric methanisation reached 91% efficiency at room temperature with an applied voltage of 1.5V using nickel cathodes. The two stage bioethanol refining process employing bioelectrochemical reactors produces more energy vectors than is possible with today's ethanol distilleries. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fast-tracking determination of homozygous transgenic lines and transgene stacking using a reliable quantitative real-time PCR assay.

PubMed

Wang, Xianghong; Jiang, Daiming; Yang, Daichang

2015-01-01

The selection of homozygous lines is a crucial step in the characterization of newly generated transgenic plants. This is particularly time- and labor-consuming when transgenic stacking is required. Here, we report a fast and accurate method based on quantitative real-time PCR with a rice gene RBE4 as a reference gene for selection of homozygous lines when using multiple transgenic stacking in rice. Use of this method allowed can be used to determine the stacking of up to three transgenes within four generations. Selection accuracy reached 100 % for a single locus and 92.3 % for two loci. This method confers distinct advantages over current transgenic research methodologies, as it is more accurate, rapid, and reliable. Therefore, this protocol could be used to efficiently select homozygous plants and to expedite time- and labor-consuming processes normally required for multiple transgene stacking. This protocol was standardized for determination of multiple gene stacking in molecular breeding via marker-assisted selection.

Partition/Ion-Exclusion Chromatographic Ion Stacking for the Analysis of Trace Anions in Water and Salt Samples by Ion Chromatography.

PubMed

Akter, Fouzia; Saito, Shingo; Tasaki-Handa, Yuiko; Shibukawa, Masami

2018-01-01

A new analytical methodology for a simple and efficient on-line preconcentration of trace inorganic anions in water and salt samples prior to ion chromatographic determination is proposed. The preconcentration method is based on partition/ion-exclusion chromatographic ion stacking (PIEC ion stacking) with a hydrophilic polymer gel column containing a small amount of fixed anionic charges. The developed on-line PIEC ion stacking-ion chromatography method was validated by recovery experiments for the determination of nitrate in tap water in terms of both accuracy and precision, and the results showed the reliability of the method. The method proposed was also successfully applied to the determination of trace impurity nitrite and nitrate in reagent-grade salts of sodium sulfate. A low background level can be achieved since pure water is used as the eluant for the PIEC ion stacking. It is possible to reach sensitive detection at sub-μg L -1 levels by on-line PIEC ion stacking-ion chromatography.

Theoretical investigation of the formation of basal plane stacking faults in heavily nitrogen-doped 4H-SiC crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taniguchi, Chisato; Ichimura, Aiko; Ohtani, Noboru, E-mail: ohtani.noboru@kwansei.ac.jp

The formation of basal plane stacking faults in heavily nitrogen-doped 4H-SiC crystals was theoretically investigated. A novel theoretical model based on the so-called quantum well action mechanism was proposed; the model considers several factors, which were overlooked in a previously proposed model, and provides a detailed explanation of the annealing-induced formation of double layer Shockley-type stacking faults in heavily nitrogen-doped 4H-SiC crystals. We further revised the model to consider the carrier distribution in the depletion regions adjacent to the stacking fault and successfully explained the shrinkage of stacking faults during annealing at even higher temperatures. The model also succeeded inmore » accounting for the aluminum co-doping effect in heavily nitrogen-doped 4H-SiC crystals, in that the stacking fault formation is suppressed when aluminum acceptors are co-doped in the crystals.« less

Study on component interface evolution of a solid oxide fuel cell stack after long term operation

NASA Astrophysics Data System (ADS)

Yang, Jiajun; Huang, Wei; Wang, Xiaochun; Li, Jun; Yan, Dong; Pu, Jian; Chi, Bo; Li, Jian

2018-05-01

A 5-cell solid oxide fuel cell (SOFC) stack with external manifold structure is assembled and underwent a durability test with an output of 250 W for nearly 4400 h when current density and operating temperature are 355 mA/cm2 and 750 °C. Cells used in the stack are anode-supported cells (ASC) with yttria-stabilized zirconia (YSZ) electrolytes, Ni/YSZ hydrogen electrodes, and YSZ based composite cathode. The dimension of the cell is 150 × 150 mm (active area: 130 × 130 mm). Ceramic-glass sealant is used in the stack to keep the gas tightness between cells, interconnects and manifolds. Pure hydrogen and dry air are used as fuel and oxidant respectively. The stack has a maximum output of 340 W at 562 mA/cm2 current density at 750 °C. The stack shows a degradation of 1.5% per 1000 h during the test with 2 thermal cycles to room temperature. After the test, the stack was dissembled and examined. The relationship between microstructure changes of interfaces and degradation in the stack are discussed. The microstructure evolution of interfaces between electrode, contact material and current collector are unveiled and their relationship with the degradation is discussed.

AlGaAs top solar cell for mechanical attachment in a multi-junction tandem concentrator solar cell stack

NASA Technical Reports Server (NTRS)

Dinetta, L. C.; Hannon, M. H.; Mcneely, J. B.; Barnett, A. M.

1991-01-01

The AstroPower self-supporting, transparent AlGaAs top solar cell can be stacked upon any well-developed bottom solar cell for improved system performance. This is an approach to improve the performance and scale of space photovoltaic power systems. Mechanically stacked tandem solar cell concentrator systems based on the AlGaAs top concentrator solar cell can provide near term efficiencies of 36 percent (AMO, 100x). Possible tandem stack efficiencies greater than 38 percent (100x, AMO) are feasible with a careful selection of materials. In a three solar cell stack, system efficiencies exceed 41 percent (100x, AMO). These device results demonstrate a practical solution for a state-of-the-art top solar cell for attachment to an existing, well-developed solar cell.

Band engineering in twisted molybdenum disulfide bilayers

NASA Astrophysics Data System (ADS)

Zhao, Yipeng; Liao, Chengwei; Ouyang, Gang

2018-05-01

In order to explore the theoretical relationship between interlayer spacing, interaction and band offset at the atomic level in vertically stacked two-dimensional (2D) van der Waals (vdW) structures, we propose an analytical model to address the evolution of interlayer vdW coupling with random stacking configurations in MoS2 bilayers based on the atomic-bond-relaxation correlation mechanism. We found that interlayer spacing changes substantially with respect to the orientations, and the bandgap increases from 1.53 eV (AB stacking) to 1.68 eV (AA stacking). Our results reveal that the evolution of interlayer vdW coupling originates from the interlayer interaction, leading to interlayer separations and electronic properties changing with stacking configurations. Our predictions constitute a demonstration of twist engineering the band shift in the emergent class of 2D crystals, transition-metal dichalcogenides.

Interfacial Stacks of Polymeric Nanofilms on Soft Biological Surfaces that Release Multiple Agents.

PubMed

Herron, Maggie; Schurr, Michael J; Murphy, Christopher J; McAnulty, Jonathan F; Czuprynski, Charles J; Abbott, Nicholas L

2016-10-03

We report a general and facile method that permits the transfer (stacking) of multiple independently fabricated and nanoscopically thin polymeric films, each containing a distinct bioactive agent, onto soft biomedically relevant surfaces (e.g., collagen-based wound dressings). By using polyelectrolyte multilayer films (PEMs) formed from poly(allyl amine hydrochloride) and poly(acrylic acid) as representative polymeric nanofilms and micrometer-thick water-soluble poly(vinyl alcohol) sacrificial films to stack the PEMs, we demonstrate that it is possible to create stacked polymeric constructs containing multiple bioactive agents (e.g., antimicrobial and antibiofilm agents) on soft and chemically complex surfaces onto which PEMs cannot be routinely transferred by stamping. We illustrate the characteristics and merits of the approach by fabricating stacks of Ga 3+ (antibiofilm agent)- and Ag + (antimicrobial agent)-loaded PEMs as prototypical examples of agent-containing PEMs and demonstrate that the stacked PEMs incorporate precise loadings of the agents and provide flexibility in terms of tuning release rates. Specifically, we show that simultaneous release of Ga 3+ and Ag + from the stacked PEMs on collagen-based wound dressings can lead to synergistic effects on bacteria, killing and dispersing biofilms formed by Pseudomonas aeruginosa (two strains: ATCC 27853 and MPAO1) at sufficiently low loadings of agents such that cytotoxic effects on mammalian cells are avoided. The approach is general (a wide range of bioactive agents other than Ga 3+ and Ag + can be incorporated into PEMs), and the modular nature of the approach potentially allows end-user functionalization of soft biological surfaces for programmed release of multiple bioactive agents.

TEM study on relationship between stacking faults and non-basal dislocations in Mg

NASA Astrophysics Data System (ADS)

Zhang, Dalong; Jiang, Lin; Schoenung, Julie M.; Mahajan, Subhash; Lavernia, Enrique J.

2015-12-01

Recent interest in the study of stacking faults and non-basal slip in Mg alloys is partly based on the argument that these phenomena positively influence mechanical behaviour. Inspection of the published literature, however, reveals that there is a lack of fundamental information on the mechanisms that govern the formation of stacking faults, especially I1-type stacking faults (I1 faults). Moreover, controversial and sometimes contradictory mechanisms have been proposed concerning the interactions between stacking faults and dislocations. Therefore, we describe a fundamental transmission electron microscope investigation on Mg 2.5 at. % Y (Mg-2.5Y) processed via hot isostatic pressing (HIP) and extrusion at 623 K. In the as-HIPed Mg-2.5Y, many and dislocations, together with some dislocations were documented, but no stacking faults were observed. In contrast, in the as-extruded Mg-2.5Y, a relatively high density of stacking faults and some non-basal dislocations were documented. Specifically, there were three different cases for the configurations of observed stacking faults. Case (I): pure I2 faults; Case (II): mixture of I1 faults and non-basal dislocations having component, together with basal dislocations; Case (III): mixture of predominant I2 faults and rare I1 faults, together with jog-like dislocation configuration. By comparing the differences in extended defect configurations, we propose three distinct stacking fault formation mechanisms for each case in the context of slip activity and point defect generation during extrusion. Furthermore, we discuss the role of stacking faults on deformation mechanisms in the context of dynamic interactions between stacking faults and non-basal slip.

3D reconstruction of the porous microstructure of Al2O3-coatings based on sequentially revealed surface data

NASA Astrophysics Data System (ADS)

Loftfield, Nina; Kästner, Markus; Reithmeier, Eduard

2018-06-01

Local and global liquid transport properties correlate strongly with the morphology of porous materials. Therefore, by characterizing the porous network information is indirectly gained on the materials properties. Properties like the open-porosity are easily accessible with techniques like mercury porosimetry. However, the 3D image reconstruction, destructive or non-destructive, holds advantages like an accurate spatially resolved representation of the investigated material. Common 3D data acquisition is done by x-ray microtomography or a combination of focused ion beam based milling and scanning electron microscopy. In this work a reconstruction approach similar to the latter one is implemented. The porous network is reconstructed based on an alternating process of milling the surface by fly cutting and measuring the surface data with a confocal laser scanning microscope. This has the benefit of reconstructing the pore network on the basis of surface height data, measuring the structure boundaries directly. The stack of milled surface height data needs to be registered and the pore structure to be segmented. The segmented pore structure is connected throughout each height layer and afterwards meshed. The investigated materials are porous surface coatings of aluminum oxide for the usage in tribological pairings.

Comparison of three methods reducing the beam parameter product of a laser diode stack for long range laser illumination applications

NASA Astrophysics Data System (ADS)

Lutz, Yves; Poyet, Jean-Michel; Metzger, Nicolas

2013-10-01

Laser diode stacks are interesting laser sources for active imaging illuminators. They allow the accumulation of large amounts of energy in multi-pulse mode, which is well suited for long-range image recording. Even when laser diode stacks are equipped with fast-axis collimation (FAC) and slow-axis collimation (SAC) microlenses, their beam parameter product (BPP) are not compatible with a direct use in highly efficient and compact illuminators. This is particularly true when narrow divergences are required such as for long range applications. To overcome these difficulties, we conducted investigations in three different ways. A first near infrared illuminator based on the use of conductively cooled mini-bars was designed, realized and successfully tested during outdoor experimentations. This custom specified stack was then replaced in a second step by an off-the-shelf FAC + SAC micro lensed stack where the brightness was increased by polarization overlapping. The third method still based on a commercial laser diode stack uses a non imaging optical shaping principle resulting in a virtually restacked laser source with enhanced beam parameters. This low cost, efficient and low alignment sensitivity beam shaping method allows obtaining a compact and high performance laser diode illuminator for long range active imaging applications. The three methods are presented and compared in this paper.

A wavelet-based Bayesian framework for 3D object segmentation in microscopy

NASA Astrophysics Data System (ADS)

Pan, Kangyu; Corrigan, David; Hillebrand, Jens; Ramaswami, Mani; Kokaram, Anil

2012-03-01

In confocal microscopy, target objects are labeled with fluorescent markers in the living specimen, and usually appear with irregular brightness in the observed images. Also, due to the existence of out-of-focus objects in the image, the segmentation of 3-D objects in the stack of image slices captured at different depth levels of the specimen is still heavily relied on manual analysis. In this paper, a novel Bayesian model is proposed for segmenting 3-D synaptic objects from given image stack. In order to solve the irregular brightness and out-offocus problems, the segmentation model employs a likelihood using the luminance-invariant 'wavelet features' of image objects in the dual-tree complex wavelet domain as well as a likelihood based on the vertical intensity profile of the image stack in 3-D. Furthermore, a smoothness 'frame' prior based on the a priori knowledge of the connections of the synapses is introduced to the model for enhancing the connectivity of the synapses. As a result, our model can successfully segment the in-focus target synaptic object from a 3D image stack with irregular brightness.

The Lopsidedness of Satellite Galaxy Systems in ΛCDM Simulations

NASA Astrophysics Data System (ADS)

Pawlowski, Marcel S.; Ibata, Rodrigo A.; Bullock, James S.

2017-12-01

The spatial distribution of satellite galaxies around pairs of galaxies in the Sloan Digital Sky Survey (SDSS) have been found to bulge significantly toward the respective partner. Highly anisotropic, planar distributions of satellite galaxies are in conflict with expectations derived from cosmological simulations. Does the lopsided distribution of satellite systems around host galaxy pairs constitute a similar challenge to the standard model of cosmology? We investigate whether such satellite distributions are present around stacked pairs of hosts extracted from the ΛCDM simulations Millennium-I, Millennium-II, Exploring the Local Volume in Simulations, and Illustris-1. By utilizing this set of simulations covering different volumes, resolutions, and physics, we implicitly test whether a lopsided signal exists for different ranges of satellite galaxy masses, and whether the inclusion of hydrodynamical effects produces significantly different results. All simulations display a lopsidedness similar to the observed situation. The signal is highly significant for simulations containing a sufficient number of hosts and resolved satellite galaxies (up to 5 σ for Millennium-II). We find a projected signal that is up to twice as strong as that reported for the SDSS systems for certain opening angles (∼16% more satellites in the direction between the pair than expected for uniform distributions). Considering that the SDSS signal is a lower limit owing to likely back- and foreground contamination, the ΛCDM simulations appear to be consistent with this particular empirical property of galaxy pairs.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2012-10-11

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

PubMed Central

Lee, Joon-Hwa; Bae, Sung-Hun; Choi, Byong-Seok

2000-01-01

In contrast to the highly mutagenic pyrimidine(6–4)pyrimidone photoproduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685–9689]. To determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW/GA duplex) contains a mismatched base pair between the 3′ T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3′ T (T6) of the Dewar lesion formed stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW/GA duplex were much larger than those of a second duplex that contains the Dewar lesion and opposing A15 and A16 residues (DW/AA duplex). The DW/GA duplex showed poorer stacking interactions at the two bases of the Dewar product and at the adjacent A7⋅T14 base pair than did the DW/AA duplex. These structural features imply that no thermal stability or conformational benefit is obtained by incorporating a G instead of an A opposite the 3′ T of the Dewar lesion. These properties may thus facilitate the preferential incorporation of an A in accordance with the A rule during translesion replication and lead to the low frequency of 3′ T→C mutations observed at this site. PMID:10758155

Staying green postharvest: how three mutations in the Arabidopsis chlorophyll b reductase gene NYC1 delay degreening by distinct mechanisms.

PubMed

Jibran, Rubina; Sullivan, Kerry L; Crowhurst, Ross; Erridge, Zoe A; Chagné, David; McLachlan, Andrew R G; Brummell, David A; Dijkwel, Paul P; Hunter, Donald A

2015-11-01

Stresses such as energy deprivation, wounding and water-supply disruption often contribute to rapid deterioration of harvested tissues. To uncover the genetic regulation behind such stresses, a simple assessment system was used to detect senescence mutants in conjunction with two rapid mapping techniques to identify the causal mutations. To demonstrate the power of this approach, immature inflorescences of Arabidopsis plants that contained ethyl methanesulfonate-induced lesions were detached and screened for altered timing of dark-induced senescence. Numerous mutant lines displaying accelerated or delayed timing of senescence relative to wild type were discovered. The underlying mutations in three of these were identified using High Resolution Melting analysis to map to a chromosomal arm followed by a whole-genome sequencing-based mapping method, termed 'Needle in the K-Stack', to identify the causal lesions. All three mutations were single base pair changes and occurred in the same gene, NON-YELLOW COLORING1 (NYC1), a chlorophyll b reductase of the short-chain dehydrogenase/reductase (SDR) superfamily. This was consistent with the mutants preferentially retaining chlorophyll b, although substantial amounts of chlorophyll b were still lost. The single base pair mutations disrupted NYC1 function by three distinct mechanisms, one by producing a termination codon, the second by interfering with correct intron splicing and the third by replacing a highly conserved proline with a non-equivalent serine residue. This non-synonymous amino acid change, which occurred in the NADPH binding domain of NYC1, is the first example of such a mutation in an SDR protein inhibiting a physiological response in plants. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Membrane adhesion dictates Golgi stacking and cisternal morphology.

PubMed

Lee, Intaek; Tiwari, Neeraj; Dunlop, Myun Hwa; Graham, Morven; Liu, Xinran; Rothman, James E

2014-02-04

Two classes of proteins that bind to each other and to Golgi membranes have been implicated in the adhesion of Golgi cisternae to each other to form their characteristic stacks: Golgi reassembly and stacking proteins 55 and 65 (GRASP55 and GRASP65) and Golgin of 45 kDa and Golgi matrix protein of 130 kDa. We report here that efficient stacking occurs in the absence of GRASP65/55 when either Golgin is overexpressed, as judged by quantitative electron microscopy. The Golgi stacks in these GRASP-deficient HeLa cells were normal both in morphology and in anterograde cargo transport. This suggests the simple hypothesis that the total amount of adhesive energy gluing cisternae dictates Golgi cisternal stacking, irrespective of which molecules mediate the adhesive process. In support of this hypothesis, we show that adding artificial adhesive energy between cisternae and mitochondria by dimerizing rapamycin-binding domain and FK506-binding protein domains that are attached to cisternal adhesive proteins allows mitochondria to invade the stack and even replace Golgi cisternae within a few hours. These results indicate that although Golgi stacking is a highly complicated process involving a large number of adhesive and regulatory proteins, the overriding principle of a Golgi stack assembly is likely to be quite simple. From this simplified perspective, we propose a model, based on cisternal adhesion and cisternal maturation as the two core principles, illustrating how the most ancient form of Golgi stacking might have occurred using only weak cisternal adhesive processes because of the differential between the rate of influx and outflux of membrane transport through the Golgi.

Membrane adhesion dictates Golgi stacking and cisternal morphology

PubMed Central

Lee, Intaek; Tiwari, Neeraj; Dunlop, Myun Hwa; Graham, Morven; Liu, Xinran; Rothman, James E.

2014-01-01

Two classes of proteins that bind to each other and to Golgi membranes have been implicated in the adhesion of Golgi cisternae to each other to form their characteristic stacks: Golgi reassembly and stacking proteins 55 and 65 (GRASP55 and GRASP65) and Golgin of 45 kDa and Golgi matrix protein of 130 kDa. We report here that efficient stacking occurs in the absence of GRASP65/55 when either Golgin is overexpressed, as judged by quantitative electron microscopy. The Golgi stacks in these GRASP-deficient HeLa cells were normal both in morphology and in anterograde cargo transport. This suggests the simple hypothesis that the total amount of adhesive energy gluing cisternae dictates Golgi cisternal stacking, irrespective of which molecules mediate the adhesive process. In support of this hypothesis, we show that adding artificial adhesive energy between cisternae and mitochondria by dimerizing rapamycin-binding domain and FK506-binding protein domains that are attached to cisternal adhesive proteins allows mitochondria to invade the stack and even replace Golgi cisternae within a few hours. These results indicate that although Golgi stacking is a highly complicated process involving a large number of adhesive and regulatory proteins, the overriding principle of a Golgi stack assembly is likely to be quite simple. From this simplified perspective, we propose a model, based on cisternal adhesion and cisternal maturation as the two core principles, illustrating how the most ancient form of Golgi stacking might have occurred using only weak cisternal adhesive processes because of the differential between the rate of influx and outflux of membrane transport through the Golgi. PMID:24449908

Retrieval of Body-Wave Reflections Using Ambient Noise Interferometry Using a Small-Scale Experiment

NASA Astrophysics Data System (ADS)

Dantas, Odmaksuel Anísio Bezerra; do Nascimento, Aderson Farias; Schimmel, Martin

2018-02-01

We report the retrieval of body-wave reflections from noise records using a small-scale experiment over a mature oil field. The reflections are obtained by cross-correlation and stacking of the data. We used the stacked correlograms to create virtual source-to-receiver common shot gathers and are able to obtain body-wave reflections. Surface waves that obliterate the body-waves in our noise correlations were attenuated following a standard procedure from active source seismics. Further different strategies were employed to cross-correlate and stack the data: classical geometrical normalized cross-correlation (CCGN), phase cross-correlation (PCC), linear stacking**** and phase weighted stacking (PWS). PCC and PWS are based on the instantaneous phase coherence of analytic signals. The four approaches are independent and reveal the reflections; nevertheless, the combination of PWS and CCGN provided the best results. Our analysis is based on 2145 cross-correlations of 600 s data segments. We also compare the resulted virtual shot gathers with an active 2D seismic line near the passive experiment. It is shown that our ambient noise analysis reproduces reflections which are present in the active seismic data.

Modelling the protocol stack in NCS with deterministic and stochastic petri net

NASA Astrophysics Data System (ADS)

Hui, Chen; Chunjie, Zhou; Weifeng, Zhu

2011-06-01

Protocol stack is the basis of the networked control systems (NCS). Full or partial reconfiguration of protocol stack offers both optimised communication service and system performance. Nowadays, field testing is unrealistic to determine the performance of reconfigurable protocol stack; and the Petri net formal description technique offers the best combination of intuitive representation, tool support and analytical capabilities. Traditionally, separation between the different layers of the OSI model has been a common practice. Nevertheless, such a layered modelling analysis framework of protocol stack leads to the lack of global optimisation for protocol reconfiguration. In this article, we proposed a general modelling analysis framework for NCS based on the cross-layer concept, which is to establish an efficiency system scheduling model through abstracting the time constraint, the task interrelation, the processor and the bus sub-models from upper and lower layers (application, data link and physical layer). Cross-layer design can help to overcome the inadequacy of global optimisation based on information sharing between protocol layers. To illustrate the framework, we take controller area network (CAN) as a case study. The simulation results of deterministic and stochastic Petri-net (DSPN) model can help us adjust the message scheduling scheme and obtain better system performance.

StackSplit - a plugin for multi-event shear wave splitting analyses in SplitLab

NASA Astrophysics Data System (ADS)

Grund, Michael

2017-08-01

SplitLab is a powerful and widely used tool for analysing seismological shear wave splitting of single event measurements. However, in many cases, especially temporary station deployments close to the noisy seaside, ocean bottom or for recordings affected by strong anthropogenic noise, only multi-event approaches provide stable and reliable splitting results. In order to extend the original SplitLab environment for such analyses, I present the StackSplit plugin that can easily be implemented within the well accepted main program. StackSplit grants easy access to several different analysis approaches within SplitLab, including a new multiple waveform based inversion method as well as the most established standard stacking procedures. The possibility to switch between different analysis approaches at any time allows the user for the most flexible processing of individual multi-event splitting measurements for a single recording station. Besides the provided functions of the plugin, no other external program is needed for the multi-event analyses since StackSplit performs within the available SplitLab structure which is based on MATLAB. The effectiveness and use of this plugin is demonstrated with data examples of a long running seismological recording station in Finland.

Reliability prediction of large fuel cell stack based on structure stress analysis

NASA Astrophysics Data System (ADS)

Liu, L. F.; Liu, B.; Wu, C. W.

2017-09-01

The aim of this paper is to improve the reliability of Proton Electrolyte Membrane Fuel Cell (PEMFC) stack by designing the clamping force and the thickness difference between the membrane electrode assembly (MEA) and the gasket. The stack reliability is directly determined by the component reliability, which is affected by the material property and contact stress. The component contact stress is a random variable because it is usually affected by many uncertain factors in the production and clamping process. We have investigated the influences of parameter variation coefficient on the probability distribution of contact stress using the equivalent stiffness model and the first-order second moment method. The optimal contact stress to make the component stay in the highest level reliability is obtained by the stress-strength interference model. To obtain the optimal contact stress between the contact components, the optimal thickness of the component and the stack clamping force are optimally designed. Finally, a detailed description is given how to design the MEA and gasket dimensions to obtain the highest stack reliability. This work can provide a valuable guidance in the design of stack structure for a high reliability of fuel cell stack.

Solid oxide fuel cell generator with removable modular fuel cell stack configurations

DOEpatents

Gillett, J.E.; Dederer, J.T.; Zafred, P.R.; Collie, J.C.

1998-04-21

A high temperature solid oxide fuel cell generator produces electrical power from oxidation of hydrocarbon fuel gases such as natural gas, or conditioned fuel gases, such as carbon monoxide or hydrogen, with oxidant gases, such as air or oxygen. This electrochemical reaction occurs in a plurality of electrically connected solid oxide fuel cells bundled and arrayed in a unitary modular fuel cell stack disposed in a compartment in the generator container. The use of a unitary modular fuel cell stack in a generator is similar in concept to that of a removable battery. The fuel cell stack is provided in a pre-assembled self-supporting configuration where the fuel cells are mounted to a common structural base having surrounding side walls defining a chamber. Associated generator equipment may also be mounted to the fuel cell stack configuration to be integral therewith, such as a fuel and oxidant supply and distribution systems, fuel reformation systems, fuel cell support systems, combustion, exhaust and spent fuel recirculation systems, and the like. The pre-assembled self-supporting fuel cell stack arrangement allows for easier assembly, installation, maintenance, better structural support and longer life of the fuel cells contained in the fuel cell stack. 8 figs.

Solid oxide fuel cell generator with removable modular fuel cell stack configurations

DOEpatents

Gillett, James E.; Dederer, Jeffrey T.; Zafred, Paolo R.; Collie, Jeffrey C.

1998-01-01

A high temperature solid oxide fuel cell generator produces electrical power from oxidation of hydrocarbon fuel gases such as natural gas, or conditioned fuel gases, such as carbon monoxide or hydrogen, with oxidant gases, such as air or oxygen. This electrochemical reaction occurs in a plurality of electrically connected solid oxide fuel cells bundled and arrayed in a unitary modular fuel cell stack disposed in a compartment in the generator container. The use of a unitary modular fuel cell stack in a generator is similar in concept to that of a removable battery. The fuel cell stack is provided in a pre-assembled self-supporting configuration where the fuel cells are mounted to a common structural base having surrounding side walls defining a chamber. Associated generator equipment may also be mounted to the fuel cell stack configuration to be integral therewith, such as a fuel and oxidant supply and distribution systems, fuel reformation systems, fuel cell support systems, combustion, exhaust and spent fuel recirculation systems, and the like. The pre-assembled self-supporting fuel cell stack arrangement allows for easier assembly, installation, maintenance, better structural support and longer life of the fuel cells contained in the fuel cell stack.

Develop and test fuel cell powered on-site integrated total energy systems: Phase 3, full-scale power plant development

NASA Technical Reports Server (NTRS)

Kaufman, A.; Pudick, S.; Wang, C. L.; Werth, J.; Whelan, J. A.

1985-01-01

A 25 cell stack of the 13 inch x 23 inch cell size (about 4kW) remains on test after 6000 hours, using simulated reformate fuel. A similar stack was previously shut down after 7000 hours on load. These tests were carried out for the purpose of assessing the durability of fuel cell stack components developed through the end of 1983. In light of the favorable results obtained, a 25kW stack that will contain 175 cells of the same size is being constructed using the same technology base. The components for the 25kW stack have been completed. A methanol steam reformer with a design output equivalent to 50kW has been constructed to serve as a hydrogen generator for the 25kW stack. This reformer and the balance of the fuel processing sub system are currently being tested and debugged. The stack technology development program focused on cost reduction in bipolar plates, nonmetallic cooling plates, and current collecting plates; more stable cathode catalyst support materials; more corrosion resistant metal hardware; and shutdown/start up tolerance.

A high-performance aluminum-feed microfluidic fuel cell stack

NASA Astrophysics Data System (ADS)

Wang, Yifei; Leung, Dennis Y. C.

2016-12-01

In this paper, a six-cell microfluidic fuel cell (MFC) stack is demonstrated. Low-cost aluminum is fed directly to the stack, which produces hydrogen fuel on site, through the Al-H2O reaction. This design is not only cost-efficient, but also eliminates the need for hydrogen storage. Unlike the conventional MFC stacks which generally require complex electrolyte distribution and management, the present Al-feed MFC stack requires only a single electrolyte stream, flowing successively through individual cells, which is finally utilized for hydrogen generation. In this manner, the whole system is greatly simplified while the operational robustness is also improved. With 2 M sodium hydroxide solution as electrolyte and kitchen foil Al as fuel, the present six-cell stack (in series) exhibits an open circuit voltage of nearly 6 V and a peak power density of 180.6 mWcm-2 at room temperature. In addition, an energy density of 1 Whg-1(Al) is achieved, which is quite high and comparable with its proton exchange membrane-based counterparts. Finally, pumpless operation of the present stack, together with its practical applications are successfully demonstrated, including lightening LED lights, driving an electric fan, and cell phone charging.

Conductance of carbon based macro-molecular structures

NASA Astrophysics Data System (ADS)

Stafström, S.; Hansson, A.; Paulsson, M.

2000-11-01

Electron transport through metallic nanotubes and stacks of wide bandgap polyaromatic hydrocarbons (PAH) are studied theoretically using the Landauer formalism. These two systems constitute examples of different types of carbon based nanostructured materials of potential use in molecular electronics. The studies are carried out for structures with finite length that bridge two contact pads. In the case of perfect metallic nanotubes, the current is observed to increase stepwise with the applied voltage and the resistance is independent on the length of the tube. In the PAH stacks, the off resonance tunneling conductance decreases exponentially with the number of molecules in the stack and shows a near linear increase with the number of carbon atoms in each molecule.

Remote direct memory access over datagrams

DOEpatents

Grant, Ryan Eric; Rashti, Mohammad Javad; Balaji, Pavan; Afsahi, Ahmad

2014-12-02

A communication stack for providing remote direct memory access (RDMA) over a datagram network is disclosed. The communication stack has a user level interface configured to accept datagram related input and communicate with an RDMA enabled network interface card (NIC) via an NIC driver. The communication stack also has an RDMA protocol layer configured to supply one or more data transfer primitives for the datagram related input of the user level. The communication stack further has a direct data placement (DDP) layer configured to transfer the datagram related input from a user storage to a transport layer based on the one or more data transfer primitives by way of a lower layer protocol (LLP) over the datagram network.

Automated manufacturing process for DEAP stack-actuators

NASA Astrophysics Data System (ADS)

Tepel, Dominik; Hoffstadt, Thorben; Maas, Jürgen

2014-03-01

Dielectric elastomers (DE) are thin polymer films belonging to the class of electroactive polymers (EAP), which are coated with compliant and conductive electrodes on each side. Due to the influence of an electrical field, dielectric elastomers perform a large amount of deformation. In this contribution a manufacturing process of automated fabricated stack-actuators based on dielectric electroactive polymers (DEAP) are presented. First of all the specific design of the considered stack-actuator is explained and afterwards the development, construction and realization of an automated manufacturing process is presented in detail. By applying this automated process, stack-actuators with reproducible and homogeneous properties can be manufactured. Finally, first DEAP actuator modules fabricated by the mentioned process are validated experimentally.

WebLogo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crooks, Gavin E.

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Sequesnce logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richermore » and more precise description of, for example, a binding site, than would a consensus sequence.« less

Multistage Force Amplification of Piezoelectric Stacks

NASA Technical Reports Server (NTRS)

Xu, Tian-Bing (Inventor); Siochi, Emilie J. (Inventor); Zuo, Lei (Inventor); Jiang, Xiaoning (Inventor); Kang, Jin Ho (Inventor)

2015-01-01

Embodiments of the disclosure include an apparatus and methods for using a piezoelectric device, that includes an outer flextensional casing, a first cell and a last cell serially coupled to each other and coupled to the outer flextensional casing such that each cell having a flextensional cell structure and each cell receives an input force and provides an output force that is amplified based on the input force. The apparatus further includes a piezoelectric stack coupled to each cell such that the piezoelectric stack of each cell provides piezoelectric energy based on the output force for each cell. Further, the last cell receives an input force that is the output force from the first cell and the last cell provides an output apparatus force In addition, the piezoelectric energy harvested is based on the output apparatus force. Moreover, the apparatus provides displacement based on the output apparatus force.

Deformation Measurement In The Hayward Fault Zone Using Partially Correlated Persistent Scatterers

NASA Astrophysics Data System (ADS)

Lien, J.; Zebker, H. A.

2013-12-01

Interferometric synthetic aperture radar (InSAR) is an effective tool for measuring temporal changes in the Earth's surface. By combining SAR phase data collected at varying times and orbit geometries, with InSAR we can produce high accuracy, wide coverage images of crustal deformation fields. Changes in the radar imaging geometry, scatterer positions, or scattering behavior between radar passes causes the measured radar return to differ, leading to a decorrelation phase term that obscures the deformation signal and prevents the use of large baseline data. Here we present a new physically-based method of modeling decorrelation from the subset of pixels with the highest intrinsic signal-to-noise ratio, the so-called persistent scatters (PS). This more complete formulation, which includes both phase and amplitude scintillations, better describes the scattering behavior of partially correlated PS pixels and leads to a more reliable selection algorithm. The new method identifies PS pixels using maximum likelihood signal-to-clutter ratio (SCR) estimation based on the joint interferometric stack phase-amplitude distribution. Our PS selection method is unique in that it considers both phase and amplitude; accounts for correlation between all possible pairs of interferometric observations; and models the effect of spatial and temporal baselines on the stack. We use the resulting maximum likelihood SCR estimate as a criterion for PS selection. We implement the partially correlated persistent scatterer technique to analyze a stack of C-band European Remote Sensing (ERS-1/2) interferometric radar data imaging the Hayward Fault Zone from 1995 to 2000. We show that our technique achieves a better trade-off between PS pixel selection accuracy and network density compared to other PS identification methods, particularly in areas of natural terrain. We then present deformation measurements obtained by the selected PS network. Our results demonstrate that the partially correlated persistent scatterer technique can attain accurate deformation measurements even in areas that suffer decorrelation due to natural terrain. The accuracy of phase unwrapping and subsequent deformation estimation on the spatially sparse PS network depends on both pixel selection accuracy and the density of the network. We find that many additional pixels can be added to the PS list if we are able to correctly identify and add those in which the scattering mechanism exhibits partial, rather than complete, correlation across all radar scenes.

Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, K.; Lipchock, S; Livingston,

2010-01-01

The bacterial second messenger c-di-GMP is used in many species to control essential processes that allow the organism to adapt to its environment. The c-di-GMP riboswitch (GEMM) is an important downstream target in this signaling pathway and alters gene expression in response to changing concentrations of c-di-GMP. The riboswitch selectively recognizes its second messenger ligand primarily through contacts with two critical nucleotides. However, these two nucleotides are not the most highly conserved residues within the riboswitch sequence. Instead, nucleotides that stack with c-di-GMP and that form tertiary RNA contacts are the most invariant. Biochemical and structural evidence reveals that themore » most common natural variants are able to make alternative pairing interactions with both guanine bases of the ligand. Additionally, a high-resolution (2.3 {angstrom}) crystal structure of the native complex reveals that a single metal coordinates the c-di-GMP backbone. Evidence is also provided that after transcription of the first nucleotide on the 3{prime}-side of the P1 helix, which is predicted to be the molecular switch, the aptamer is functional for ligand binding. Although large energetic effects occur when several residues in the RNA are altered, mutations at the most conserved positions, rather than at positions that base pair with c-di-GMP, have the most detrimental effects on binding. Many mutants retain sufficient c-di-GMP affinity for the RNA to remain biologically relevant, which suggests that this motif is quite resilient to mutation.« less

Positron source position sensing detector and electronics

DOEpatents

Burnham, Charles A.; Bradshaw, Jr., John F.; Kaufman, David E.; Chesler, David A.; Brownell, Gordon L.

1985-01-01

A positron source, position sensing device, particularly with medical applications, in which positron induced gamma radiation is detected using a ring of stacked, individual scintillation crystals, a plurality of photodetectors, separated from the scintillation crystals by a light guide, and high resolution position interpolation electronics. Preferably the scintillation crystals are several times more numerous than the photodetectors with each crystal being responsible for a single scintillation event from a received gamma ray. The light guide will disperse the light emitted from gamma ray absorption over several photodetectors. Processing electronics for the output of the photodetectors resolves the location of the scintillation event to a fraction of the dimension of each photodetector. Because each positron absorption results in two 180.degree. oppositely traveling gamma rays, the detection of scintillation in pairs permits location of the positron source in a manner useful for diagnostic purposes. The processing electronics simultaneously responds to the outputs of the photodetectors to locate the scintillations to the source crystal. While it is preferable that the scintillation crystal include a plurality of stacked crystal elements, the resolving power of the processing electronics is also applicable to continuous crystal scintillators.

Refocusing distance of a standard plenoptic camera.

PubMed

Hahne, Christopher; Aggoun, Amar; Velisavljevic, Vladan; Fiebig, Susanne; Pesch, Matthias

2016-09-19

Recent developments in computational photography enabled variation of the optical focus of a plenoptic camera after image exposure, also known as refocusing. Existing ray models in the field simplify the camera's complexity for the purpose of image and depth map enhancement, but fail to satisfyingly predict the distance to which a photograph is refocused. By treating a pair of light rays as a system of linear functions, it will be shown in this paper that its solution yields an intersection indicating the distance to a refocused object plane. Experimental work is conducted with different lenses and focus settings while comparing distance estimates with a stack of refocused photographs for which a blur metric has been devised. Quantitative assessments over a 24 m distance range suggest that predictions deviate by less than 0.35 % in comparison to an optical design software. The proposed refocusing estimator assists in predicting object distances just as in the prototyping stage of plenoptic cameras and will be an essential feature in applications demanding high precision in synthetic focus or where depth map recovery is done by analyzing a stack of refocused photographs.

EUVL mask patterning with blanks from commercial suppliers

NASA Astrophysics Data System (ADS)

Yan, Pei-Yang; Zhang, Guojing; Nagpal, Rajesh; Shu, Emily Y.; Li, Chaoyang; Qu, Ping; Chen, Frederick T.

2004-12-01

Extreme Ultraviolet Lithography (EUVL) reflective mask blank development includes low thermal expansion material fabrication, mask substrate finishing, reflective multi-layer (ML) and capping layer deposition, buffer (optional)/absorber stack deposition, EUV specific metrology, and ML defect inspection. In the past, we have obtained blanks deposited with various layer stacks from several vendors. Some of them are not commercial suppliers. As a result, the blank and patterned mask qualities are difficult to maintain and improve. In this paper we will present the evaluation results of the EUVL mask pattering processes with the complete EUVL mask blanks supplied by the commercial blank supplier. The EUVL mask blanks used in this study consist of either quartz or ULE substrates which is a type of low thermal expansion material (LTEM), 40 pairs of molybdenum/silicon (Mo/Si) ML layer, thin ruthenium (Ru) capping layer, tantalum boron nitride (TaBN) absorber, and chrome (Cr) backside coating. No buffer layer is used. Our study includes the EUVL mask blank characterization, patterned EUVL mask characterization, and the final patterned EUVL mask flatness evaluation.

Resolving the structure of Ti 3C 2T x MXenes through multilevel structural modeling of the atomic pair distribution function

DOE PAGES

Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; ...

2015-12-08

MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and great promise in energy storage and many other applications. But, a complex surface chemistry and small coherence length have been obstacles in some applications of MXenes, also limiting the accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti 3C 2T x MXenesmore » (T stands for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. We present the true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed “third-generation” structure model. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical, and functional properties of Ti 3C 2-based MXenes. Moreover, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical, and other properties. Finally, we suggest that the multilevel structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.« less

NUCLEAR REACTORS

DOEpatents

Long, E.; Ashley, J.W.

1958-12-16

A graphite moderator structure is described for a gas-cooled nuclear reactor having a vertical orlentation wherein the structure is physically stable with regard to dlmensional changes due to Wigner growth properties of the graphite, and leakage of coolant gas along spaces in the structure is reduced. The structure is comprised of stacks of unlform right prismatic graphite blocks positioned in layers extending in the direction of the lengths of the blocks, the adjacent end faces of the blocks being separated by pairs of tiles. The blocks and tiles have central bores which are in alignment when assembled and are provided with cooperatlng keys and keyways for physical stability.

N-(1-Allyl-3-chloro-4-eth­oxy-1H-indazol-5-yl)-4-methyl­benzene­sulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2014-01-01

In the title compound, C19H20ClN3O3S, the benzene ring is inclined to the indazole ring system by 51.23 (8)°. In the crystal, mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers which stack in columns parallel to [011]. The atoms in the allyl group are disordered over two sets of sites with an occupancy ratio of 0.624 (8):0.376 (8). PMID:24940237

Stacking of purines in water: the role of dipolar interactions in caffeine.

PubMed

Tavagnacco, L; Di Fonzo, S; D'Amico, F; Masciovecchio, C; Brady, J W; Cesàro, A

2016-05-11

During the last few decades it has been ascertained that base stacking is one of the major contributions stabilizing nucleic acid conformations. However, the understanding of the nature of the interactions involved in the stacking process remains under debate and it is a subject of theoretical and experimental studies. Structural similarity between purine bases (guanine and adenine) in DNA and the caffeine molecule makes caffeine an excellent model for the purine bases. The present study clearly shows that dipolar interactions play a fundamental role in determining stacking of purine molecules in solution. In order to reach this achievement, polarized ultraviolet Raman resonant scattering experiments have been carried out on caffeine aqueous solutions as a function of concentration and temperature. The investigation pointed out at the aggregation and solvation properties, particularly at elevated temperatures. Kubo-Anderson theory was used as a framework to investigate the non-coincidence effect (NCE) occurring in the totally symmetric breathing modes of the purine rings, and in the bending modes of the methyl groups of caffeine. The NCE concentration dependence shows that caffeine aggregation at 80 °C occurs by planar stacking of the hydrophobic faces. The data clearly indicate that dipolar interactions determine the reorientational motion of the molecules in solution and are the driving force for the stacking of caffeine. In parallel, the observed dephasing times imply a change in caffeine interactions as a function of temperature and concentration. A decrease, at low water content, of the dephasing time for the ring breathing vibration mode indicates that self-association alters the solvation structure that is detectable at low concentration. These results are in agreement with simulation predictions and serve as an important validation of the models used in those calculations.

Monolithic stacked blue light-emitting diodes with polarization-enhanced tunnel junctions.

PubMed

Kuo, Yen-Kuang; Shih, Ya-Hsuan; Chang, Jih-Yuan; Lai, Wei-Chih; Liu, Heng; Chen, Fang-Ming; Lee, Ming-Lun; Sheu, Jinn-Kong

2017-08-07

Monolithic stacked InGaN light-emitting diode (LED) connected by a polarization-enhanced GaN/AlN-based tunnel junction is demonstrated experimentally in this study. The typical stacked LEDs exhibit 80% enhancement in output power compared with conventional single LEDs because of the repeated use of electrons and holes for photon generation. The typical operation voltage of stacked LEDs is higher than twice the operation voltage of single LEDs. This high operation voltage can be attributed to the non-optimal tunneling junction in stacked LEDs. In addition to the analyses of experimental results, theoretical analysis of different schemes of tunnel junctions, including diagrams of energy bands, diagrams of electric fields, and current-voltage relation curves, are investigated using numerical simulation. The results shown in this paper demonstrate the feasibility in developing cost-effective and highly efficient tunnel-junction LEDs.

Umbilical mechanism

NASA Technical Reports Server (NTRS)

Barron, Daniel R. (Inventor); Jasulaitis, Vytas (Inventor); Morrill, Brion F. (Inventor)

1995-01-01

Apparatus is described for automatically mating a pair of connectors and protecting them prior to mating, which minimizes weight and uses relatively simple and reliable mechanisms. Lower and upper connectors (24, 26) are held in lower and upper parts (14, 16) of a housing, with the upper connector mounted on a carrier (32) that is motor driven to move down and mate the connectors. A pair of movable members (36, 38) serve as shields, as coarse alignment aids, and as force transmitters. The movable members are pivotally mounted at the bottom of the upper housing, and as the carrier moves down it pivots the members out of the way. The movable members have socket elements (116) that closely receive pin elements (120) on the lower housing part, to coarsely align the connectors and to react mating and unmating forces between the housings. The carrier has a pair of plate portions (60, 62) with slots (64), and the movable members have cam followers engaged with the slot walls, to move the members with precision. The carrier plate-like portions engage follower members (82) that pivot open lower shield parts (44, 46) covering the lower connector, which is mounted on four stacks of Belleville washers (142).

Electrical Generation for More-Electric Aircraft Using Solid Oxide Fuel Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whyatt, Greg A.; Chick, Lawrence A.

This report examines the potential for Solid-Oxide Fuel Cells (SOFC) to provide electrical generation on-board commercial aircraft. Unlike a turbine-based auxiliary power unit (APU) a solid oxide fuel cell power unit (SOFCPU) would be more efficient than using the main engine generators to generate electricity and would operate continuously during flight. The focus of this study is on more-electric aircraft which minimize bleed air extraction from the engines and instead use electrical power obtained from generators driven by the main engines to satisfy all major loads. The increased electrical generation increases the potential fuel savings obtainable through more efficient electricalmore » generation using a SOFCPU. However, the weight added to the aircraft by the SOFCPU impacts the main engine fuel consumption which reduces the potential fuel savings. To investigate these relationships the Boeing 787­8 was used as a case study. The potential performance of the SOFCPU was determined by coupling flowsheet modeling using ChemCAD software with a stack performance algorithm. For a given stack operating condition (cell voltage, anode utilization, stack pressure, target cell exit temperature), ChemCAD software was used to determine the cathode air rate to provide stack thermal balance, the heat exchanger duties, the gross power output for a given fuel rate, the parasitic power for the anode recycle blower and net power obtained from (or required by) the compressor/expander. The SOFC is based on the Gen4 Delphi planar SOFC with assumed modifications to tailor it to this application. The size of the stack needed to satisfy the specified condition was assessed using an empirically-based algorithm. The algorithm predicts stack power density based on the pressure, inlet temperature, cell voltage and anode and cathode inlet flows and compositions. The algorithm was developed by enhancing a model for a well-established material set operating at atmospheric pressure to reflect the effect of elevated pressure and to represent the expected enhancement obtained using a promising cell material set which has been tested in button cells but not yet used to produce full-scale stacks. The predictions for the effect of pressure on stack performance were based on literature. As part of this study, additional data were obtained on button cells at elevated pressure to confirm the validity of the predictions. The impact of adding weight to the 787-8 fuel consumption was determined as a function of flight distance using a PianoX model. A conceptual design for a SOFC power system for the Boeing 787 is developed and the weight estimated. The results indicate that the power density of the stacks must increase by at least a factor of 2 to begin saving fuel on the 787 aircraft. However, the conceptual design of the power system may still be useful for other applications which are less weight sensitive.« less

Compact piezoelectric tripod manipulator based on a reverse bridge-type amplification mechanism

NASA Astrophysics Data System (ADS)

Na, Tae-Won; Choi, Jun-Ho; Jung, Jin-Young; Kim, Hyeong-Geon; Han, Jae-Hung; Park, Kwang-Chun; Oh, Il-Kwon

2016-09-01

We report a hierarchical piezoelectric tripod manipulator based on a reverse bridge-type displacement amplifier. The reverse bridge-type amplification mechanism is pre-strained by each piezo-stack actuator up to 60 μm and is cross-stacked in a series arrangement to make a compact and high-stroke manipulator having load-bearing characteristics. The designed manipulator with three degrees of freedom is compact with a height of 56.0 mm, a diameter of 48.6 mm and total weight of 115 g. It achieves a translational stroke of up to 880 μm in heaving motion and a tilting angle of up to 2.0° in rotational motion within the operating voltage and power range of the piezoelectric stack actuator. A key feature of the present design is built-in and pre-strained displacement amplification mechanisms integrated with piezoelectric stacked actuators, resulting in a compact tripod manipulator having exceptionally high stroke and load-bearing capacity.

DNA Charge Transport: From Chemical Principles to the Cell

PubMed Central

Arnold, Anna R.; Grodick, Michael A.; Barton, Jacqueline K.

2016-01-01

The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology. PMID:26933744

Thin Co/Ni-based bottom pinned spin-transfer torque magnetic random access memory stacks with high annealing tolerance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomczak, Y., E-mail: Yoann.Tomczak@imec.be; Department of Chemistry, KU Leuven; Swerts, J.

2016-01-25

Spin-transfer torque magnetic random access memory (STT-MRAM) is considered as a replacement for next generation embedded and stand-alone memory applications. One of the main challenges in the STT-MRAM stack development is the compatibility of the stack with CMOS process flows in which thermal budgets up to 400 °C are applied. In this letter, we report on a perpendicularly magnetized MgO-based tunnel junction (p-MTJ) on a thin Co/Ni perpendicular synthetic antiferromagnetic layer with high annealing tolerance. Tunnel magneto resistance (TMR) loss after annealing occurs when the reference layer loses its perpendicular magnetic anisotropy due to reduction of the CoFeB/MgO interfacial anisotropy. Amore » stable Co/Ni based p-MTJ stack with TMR values of 130% at resistance-area products of 9 Ω μm{sup 2} after 400 °C anneal is achieved via moment control of the Co/Ta/CoFeB reference layer. Thinning of the CoFeB polarizing layer down to 0.8 nm is the key enabler to achieve 400 °C compatibility with limited TMR loss. Thinning the Co below 0.6 nm leads to a loss of the antiferromagnetic interlayer exchange coupling strength through Ru. Insight into the thickness and moment engineering of the reference layer is displayed to obtain the best magnetic properties and high thermal stability for thin Co/Ni SAF-based STT-MRAM stacks.« less

Reliability analysis and initial requirements for FC systems and stacks

NASA Astrophysics Data System (ADS)

Åström, K.; Fontell, E.; Virtanen, S.

In the year 2000 Wärtsilä Corporation started an R&D program to develop SOFC systems for CHP applications. The program aims to bring to the market highly efficient, clean and cost competitive fuel cell systems with rated power output in the range of 50-250 kW for distributed generation and marine applications. In the program Wärtsilä focuses on system integration and development. System reliability and availability are key issues determining the competitiveness of the SOFC technology. In Wärtsilä, methods have been implemented for analysing the system in respect to reliability and safety as well as for defining reliability requirements for system components. A fault tree representation is used as the basis for reliability prediction analysis. A dynamic simulation technique has been developed to allow for non-static properties in the fault tree logic modelling. Special emphasis has been placed on reliability analysis of the fuel cell stacks in the system. A method for assessing reliability and critical failure predictability requirements for fuel cell stacks in a system consisting of several stacks has been developed. The method is based on a qualitative model of the stack configuration where each stack can be in a functional, partially failed or critically failed state, each of the states having different failure rates and effects on the system behaviour. The main purpose of the method is to understand the effect of stack reliability, critical failure predictability and operating strategy on the system reliability and availability. An example configuration, consisting of 5 × 5 stacks (series of 5 sets of 5 parallel stacks) is analysed in respect to stack reliability requirements as a function of predictability of critical failures and Weibull shape factor of failure rate distributions.

Ab initio study of point defects near stacking faults in 3C-SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xi, Jianqi; Liu, Bin; Zhang, Yanwen

Interactions between point defects and stacking faults in 3C-SiC are studied using an ab initio method based on density functional theory. The results show that the discontinuity of the stacking sequence considerably affects the configurations and behavior of intrinsic defects, especially in the case of silicon interstitials. The existence of an intrinsic stacking fault (missing a C-Si bilayer) shortens the distance between the tetrahedral-center site and its second-nearest-neighboring silicon layer, making the tetrahedral silicon interstitial unstable. Instead of a tetrahedral configuration with four C neighbors, a pyramid-like interstitial structure with a defect state within the band gap becomes a stablemore » configuration. In addition, orientation rotation occurs in the split interstitials that has diverse effects on the energy landscape of silicon and carbon split interstitials in the stacking fault region. Moreover, our analyses of ionic relaxation and electronic structure of vacancies show that the built-in strain field, owing to the existence of the stacking fault, makes the local environment around vacancies more complex than that in the bulk.« less

Ab initio study of point defects near stacking faults in 3C-SiC

DOE PAGES

Xi, Jianqi; Liu, Bin; Zhang, Yanwen; ...

2016-07-02

Interactions between point defects and stacking faults in 3C-SiC are studied using an ab initio method based on density functional theory. The results show that the discontinuity of the stacking sequence considerably affects the configurations and behavior of intrinsic defects, especially in the case of silicon interstitials. The existence of an intrinsic stacking fault (missing a C-Si bilayer) shortens the distance between the tetrahedral-center site and its second-nearest-neighboring silicon layer, making the tetrahedral silicon interstitial unstable. Instead of a tetrahedral configuration with four C neighbors, a pyramid-like interstitial structure with a defect state within the band gap becomes a stablemore » configuration. In addition, orientation rotation occurs in the split interstitials that has diverse effects on the energy landscape of silicon and carbon split interstitials in the stacking fault region. Moreover, our analyses of ionic relaxation and electronic structure of vacancies show that the built-in strain field, owing to the existence of the stacking fault, makes the local environment around vacancies more complex than that in the bulk.« less

Optimization of hole generation in Ti/CFRP stacks

NASA Astrophysics Data System (ADS)

Ivanov, Y. N.; Pashkov, A. E.; Chashhin, N. S.

2018-03-01

The article aims to describe methods for improving the surface quality and hole accuracy in Ti/CFRP stacks by optimizing cutting methods and drill geometry. The research is based on the fundamentals of machine building, theory of probability, mathematical statistics, and experiment planning and manufacturing process optimization theories. Statistical processing of experiment data was carried out by means of Statistica 6 and Microsoft Excel 2010. Surface geometry in Ti stacks was analyzed using a Taylor Hobson Form Talysurf i200 Series Profilometer, and in CFRP stacks - using a Bruker ContourGT-Kl Optical Microscope. Hole shapes and sizes were analyzed using a Carl Zeiss CONTURA G2 Measuring machine, temperatures in cutting zones were recorded with a FLIR SC7000 Series Infrared Camera. Models of multivariate analysis of variance were developed. They show effects of drilling modes on surface quality and accuracy of holes in Ti/CFRP stacks. The task of multicriteria drilling process optimization was solved. Optimal cutting technologies which improve performance were developed. Methods for assessing thermal tool and material expansion effects on the accuracy of holes in Ti/CFRP/Ti stacks were developed.

Application of preconditioned alternating direction method of multipliers in depth from focal stack

NASA Astrophysics Data System (ADS)

Javidnia, Hossein; Corcoran, Peter

2018-03-01

Postcapture refocusing effect in smartphone cameras is achievable using focal stacks. However, the accuracy of this effect is totally dependent on the combination of the depth layers in the stack. The accuracy of the extended depth of field effect in this application can be improved significantly by computing an accurate depth map, which has been an open issue for decades. To tackle this issue, a framework is proposed based on a preconditioned alternating direction method of multipliers for depth from the focal stack and synthetic defocus application. In addition to its ability to provide high structural accuracy, the optimization function of the proposed framework can, in fact, converge faster and better than state-of-the-art methods. The qualitative evaluation has been done on 21 sets of focal stacks and the optimization function has been compared against five other methods. Later, 10 light field image sets have been transformed into focal stacks for quantitative evaluation purposes. Preliminary results indicate that the proposed framework has a better performance in terms of structural accuracy and optimization in comparison to the current state-of-the-art methods.

Advancements in high-power diode laser stacks for defense applications

NASA Astrophysics Data System (ADS)

Pandey, Rajiv; Merchen, David; Stapleton, Dean; Patterson, Steve; Kissel, Heiko; Fassbender, Wilhlem; Biesenbach, Jens

2012-06-01

This paper reports on the latest advancements in vertical high-power diode laser stacks using micro-channel coolers, which deliver the most compact footprint, power scalability and highest power/bar of any diode laser package. We present electro-optical (E-O) data on water-cooled stacks with wavelengths ranging from 7xx nm to 9xx nm and power levels of up to 5.8kW, delivered @ 200W/bar, CW mode, and a power-conversion efficiency of >60%, with both-axis collimation on a bar-to-bar pitch of 1.78mm. Also, presented is E-O data on a compact, conductively cooled, hardsoldered, stack package based on conventional CuW and AlN materials, with bar-to-bar pitch of 1.8mm, delivering average power/bar >15W operating up to 25% duty cycle, 10ms pulses @ 45C. The water-cooled stacks can be used as pump-sources for diode-pumped alkali lasers (DPALs) or for more traditional diode-pumped solid-state lasers (DPSSL). which are power/brightness scaled for directed energy weapons applications and the conductively-cooled stacks as illuminators.

Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections.

PubMed

Schneebeli, Severin T; Kamenetska, Maria; Cheng, Zhanling; Skouta, Rachid; Friesner, Richard A; Venkataraman, Latha; Breslow, Ronald

2011-02-23

Understanding electron transport across π-π-stacked systems will help to answer fundamental questions about biochemical redox processes and benefit the design of new materials and molecular devices. Herein we employed the STM break-junction technique to measure the single-molecule conductance of multiple π-π-stacked aromatic rings. We studied electron transport through up to four stacked benzene rings held together in an eclipsed fashion via a paracyclophane scaffold. We found that the strained hydrocarbons studied herein couple directly to gold electrodes during the measurements; hence, we did not require any heteroatom binding groups as electrical contacts. Density functional theory-based calculations suggest that the gold atoms of the electrodes bind to two neighboring carbon atoms of the outermost cyclophane benzene rings in η(2) fashion. Our measurements show an exponential decay of the conductance with an increasing number of stacked benzene rings, indicating a nonresonant tunneling mechanism. Furthermore, STM tip-substrate displacement data provide additional evidence that the electrodes bind to the outermost benzene rings of the π-π-stacked molecular wires.

Model predictive control of the solid oxide fuel cell stack temperature with models based on experimental data

NASA Astrophysics Data System (ADS)

Pohjoranta, Antti; Halinen, Matias; Pennanen, Jari; Kiviaho, Jari

2015-03-01

Generalized predictive control (GPC) is applied to control the maximum temperature in a solid oxide fuel cell (SOFC) stack and the temperature difference over the stack. GPC is a model predictive control method and the models utilized in this work are ARX-type (autoregressive with extra input), multiple input-multiple output, polynomial models that were identified from experimental data obtained from experiments with a complete SOFC system. The proposed control is evaluated by simulation with various input-output combinations, with and without constraints. A comparison with conventional proportional-integral-derivative (PID) control is also made. It is shown that if only the stack maximum temperature is controlled, a standard PID controller can be used to obtain output performance comparable to that obtained with the significantly more complex model predictive controller. However, in order to control the temperature difference over the stack, both the stack minimum and the maximum temperature need to be controlled and this cannot be done with a single PID controller. In such a case the model predictive controller provides a feasible and effective solution.

Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions.

PubMed

Biswas, Sovan; Sen, Suman; Im, JongOne; Biswas, Sudipta; Krstic, Predrag; Ashcroft, Brian; Borges, Chad; Zhao, Yanan; Lindsay, Stuart; Zhang, Peiming

2016-12-27

A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1 H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.

A disposable power source in resource-limited environments: A paper-based biobattery generating electricity from wastewater.

PubMed

Fraiwan, Arwa; Kwan, Landen; Choi, Seokheun

2016-11-15

We report a novel paper-based biobattery which generates power from microorganism-containing liquid derived from renewable and sustainable wastewater which is readily accessible in the local environment. The device fuses the art of origami and the technology of microbial fuel cells (MFCs) and has the potential to shift the paradigm for flexible and stackable paper-based batteries by enabling exceptional electrical characteristics and functionalities. 3D, modular, and retractable battery stack is created from (i) 2D paper sheets through high degrees of folding and (ii) multifunctional layers sandwiched for MFC device configuration. The stack is based on ninja star-shaped origami design formed by eight MFC modular blades, which is retractable from sharp shuriken (closed) to round frisbee (opened). The microorganism-containing wastewater is added into an inlet of the closed battery stack and it is transported into each MFC module through patterned fluidic pathways in the paper layers. During operation, the battery stack is transformed into the round frisbee to connect eight MFC modules in series for improving the power output and simultaneously expose all air-cathodes to the air for their cathodic reactions. The device generates desired values of electrical current and potential for powering an LED for more than 20min. Copyright © 2016 Elsevier B.V. All rights reserved.

Plants with stacked genetically modified events: to assess or not to assess?

PubMed

Kok, Esther J; Pedersen, Jan; Onori, Roberta; Sowa, Slawomir; Schauzu, Marianna; De Schrijver, Adinda; Teeri, Teemu H

2014-02-01

The principles for the safety assessment of genetically modified (GM) organisms (GMOs) are harmonised worldwide to a large extent. There are, however, still differences between the European GMO regulations and the GMO regulations as they have been formulated in other parts of the world. One of these differences relates to the so-called 'stacked GM events', that is, GMOs, plants so far, where new traits are combined by conventional crossing of different GM plants. This paper advocates rethinking the current food/feed safety assessment of stacked GM events in Europe based on an analysis of different aspects that currently form the rationale for the safety assessment of stacked GM events. Copyright © 2013 Elsevier Ltd. All rights reserved.

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases†

PubMed Central

Liang, JingXin; Nguyen, Quynh L.; Matsika, Spiridoula

2016-01-01

Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids’ structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process. PMID:23625036

A study of swing-curve physics in diffraction-based overlay

NASA Astrophysics Data System (ADS)

Bhattacharyya, Kaustuve; den Boef, Arie; Storms, Greet; van Heijst, Joost; Noot, Marc; An, Kevin; Park, Noh-Kyoung; Jeon, Se-Ra; Oh, Nang-Lyeom; McNamara, Elliott; van de Mast, Frank; Oh, SeungHwa; Lee, Seung Yoon; Hwang, Chan; Lee, Kuntack

2016-03-01

With the increase of process complexity in advanced nodes, the requirements of process robustness in overlay metrology continues to tighten. Especially with the introduction of newer materials in the film-stack along with typical stack variations (thickness, optical properties, profile asymmetry etc.), the signal formation physics in diffraction-based overlay (DBO) becomes an important aspect to apply in overlay metrology target and recipe selection. In order to address the signal formation physics, an effort is made towards studying the swing-curve phenomena through wavelength and polarizations on production stacks using simulations as well as experimental technique using DBO. The results provide a wealth of information on target and recipe selection for robustness. Details from simulation and measurements will be reported in this technical publication.

The development of estimated methodology for interfacial adhesion of semiconductor coatings having an enormous mismatch extent

NASA Astrophysics Data System (ADS)

Lee, Chang-Chun; Huang, Pei-Chen

2018-05-01

The long-term reliability of multi-stacked coatings suffering the bending or rolling load was a severe challenge to extend the lifespan of foregoing structure. In addition, the adhesive strength of dissimilar materials was regarded as the major mechanical reliability concerns among multi-stacked films. However, the significant scale-mismatch from several nano-meter to micro-meter among the multi-stacked coatings causing the numerical accuracy and converged capability issues on fracture-based simulation approach. For those reasons, this study proposed the FEA-based multi-level submodeling and multi-point constraint (MPC) technique to conquer the foregoing scale-mismatch issue. The results indicated that the decent region of first and second-order submodeling can achieve the small error of 1.27% compared with the experimental result and significantly reduced the mesh density and computing time. Moreover, the MPC method adopted in FEA simulation also shown only 0.54% error when the boundary of selected local region was away the concerned critical region following the Saint-Venant principle. In this investigation, two FEA-based approaches were used to conquer the evidently scale mismatch issue when the adhesive strengths of micro and nano-scale multi-stacked coating were taken into account.

Design trade-offs among shunt current, pumping loss and compactness in the piping system of a multi-stack vanadium flow battery

NASA Astrophysics Data System (ADS)

Ye, Qiang; Hu, Jing; Cheng, Ping; Ma, Zhiqi

2015-11-01

Trade-off between shunt current loss and pumping loss is a major challenge in the design of the electrolyte piping network in a flow battery system. It is generally recognized that longer and thinner ducts are beneficial to reduce shunt current but detrimental to minimize pumping power. Base on the developed analog circuit model and the flow network model, we make case studies of multi-stack vanadium flow battery piping systems and demonstrate that both shunt current and electrolyte flow resistance can be simultaneously minimized by using longer and thicker ducts in the piping network. However, extremely long and/or thick ducts lead to a bulky system and may be prohibited by the stack structure. Accordingly, the intrinsic design trade-off is between system efficiency and compactness. Since multi-stack configurations bring both flexibility and complexity to the design process, we perform systematic comparisons among representative piping system designs to illustrate the complicated trade-offs among numerous parameters including stack number, intra-stack channel resistance and inter-stack pipe resistance. As the final design depends on various technical and economical requirements, this paper aims to provide guidelines rather than solutions for designers to locate the optimal trade-off points according to their specific cases.

Investigation of Ruthenium Dissolution in Advanced Membrane Electrode Assemblies for Direct Methanol Based Fuel Cell Stacks

NASA Technical Reports Server (NTRS)

Valdez, Thomas I.; Firdosy, S.; Koel, B. E.; Narayanan, S. R.

2005-01-01

Dissolution of ruthenium was observed in the 80-cell stack. Duration testing was performed in single cell MEAs to determine the pathway of cell degradation. EDAX analysis on each of the single cell MEAs has shown that the Johnson Matthey commercial catalyst is stable in DMFC operation for 250 hours, no ruthenium dissolution was observed. Changes in the hydrophobicity of the cathode backing papers was minimum. Electrode polarization analysis revealed that the MEA performance loss is attributed to changes in the cathode catalyst layer. Ruthenium migration does not seem to occur during cell operation but can occur when methanol is absent from the anode compartment, the cathode compartment has access to air, and the cells in the stack are electrically connected to a load (Shunt Currents). The open-to-air cathode stack design allowed for: a) The MEAs to have continual access to oxygen; and b) The stack to sustain shunt currents. Ruthenium dissolution in a DMFC stack can be prevented by: a) Developing an internally manifolded stacks that seal reactant compartments when not in operation; b) Bringing the cell voltages to zero quickly when not in operation; and c) Limiting the total number of cells to 25 in an effort to limit shunt currents.

Assessment of the LV-C2 Stack Sampling Probe Location for Compliance with ANSI/HPS N13.1-1999

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glissmeyer, John A.; Antonio, Ernest J.; Flaherty, Julia E.

2015-09-01

This document reports on a series of tests conducted to assess the proposed air sampling location for the Hanford Tank Waste Treatment and Immobilization Plant (WTP) Low-Activity Waste (LAW) C2V (LV-C2) exhaust stack with respect to the applicable criteria regarding the placement of an air sampling probe. Federal regulations require that a sampling probe be located in the exhaust stack according to the criteria established by the American National Standards Institute/Health Physics Society (ANSI/HPS) N13.1-1999, Sampling and Monitoring Releases of Airborne Radioactive Substances from the Stack and Ducts of Nuclear Facilities. These criteria address the capability of the sampling probemore » to extract a sample that represents the effluent stream. The tests were conducted on the LV-C2 scale model system. Based on the scale model tests, the location proposed for the air sampling probe in the scale model stack meets the requirements of the ANSI/HPS N13.1-1999 standard for velocity uniformity, flow angle, gas tracer and particle tracer uniformity. Additional velocity uniformity and flow angle tests on the actual stack will be necessary during cold startup to confirm the validity of the scale model results in representing the actual stack.« less

Electrical power from sea and river water by reverse electrodialysis: a first step from the laboratory to a real power plant.

PubMed

Veerman, Joost; Saakes, Michel; Metz, Sybrand J; Harmsen, G Jan

2010-12-01

Electricity can be produced directly with reverse electrodialysis (RED) from the reversible mixing of two solutions of different salinity, for example, sea and river water. The literature published so far on RED was based on experiments with relatively small stacks with cell dimensions less than 10 × 10 cm(2). For the implementation of the RED technique, it is necessary to know the challenges associated with a larger system. In the present study we show the performance of a scaled-up RED stack, equipped with 50 cells, each measuring 25 × 75 cm(2). A single cell consists of an AEM (anion exchange membrane) and a CEM (cation exchange membrane) and therefore, the total active membrane area in the stack is 18.75 m(2). This is the largest dimension of a reverse electrodialysis stack published so far. By comparing the performance of this stack with a small stack (10 × 10 cm(2), 50 cells) it was found that the key performance parameter to maximal power density is the hydrodynamic design of the stack. The power densities of the different stacks depend on the residence time of the fluids in the stack. For the large stack this was negatively affected by the increased hydrodynamic losses due to the longer flow path. It was also found that the large stack generated more power when the sea and river water were flowing in co-current operation. Co-current flow has other advantages, the local pressure differences between sea and river water compartments are low, hence preventing leakage around the internal manifolds and through pinholes in the membranes. Low pressure differences also enable the use of very thin membranes (with low electrical resistance) as well as very open spacers (with low hydrodynamic losses) in the future. Moreover, we showed that the use of segmented electrodes increase the power output by 11%.

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the parameter values for each operation. The knowledge of CRS-Stack processing procedure is still preserved in the software, which is easy and efficient to be learned. The software will still be developed in the future. Any new innovative seismic processing workflow will also be added into this GUI software.

Dual control of low concentration CO poisoning by anode air bleeding of low temperature polymer electrolyte membrane fuel cells

NASA Astrophysics Data System (ADS)

Klages, Merle; Tjønnås, Johannes; Zenith, Federico; Halvorsen, Ivar J.; Scholta, Joachim

2016-12-01

Fuel impurities, fed to a polymer electrolyte membrane fuel cell, can affect stack performance by poisoning of catalyst layers. This paper describes the dynamic behaviour of a stack, including state-of-the-art membrane electrode assemblies (MEA) of three different manufacturers, at different operating conditions. The voltage transients of the step responses to CO poisoning as well as air bleed recovery are compared, revealing differences in performance loss: slow poisoning versus fast recovery, incomplete recovery and voltage oscillation. The recorded behaviour is used to develop a model, based on Tafel equation and first order dynamic response, which can be calibrated to each MEA type. Using this model to predict voltage response, a controller is built with the aim of reducing the total amount of air bleed and monitoring upstream stack processes without the need of sensors measuring the poisoning level. Two controllers are implemented in order to show the concept from a heuristic, easy to implement, and a more technical side allowing more detailed analysis of the synthesis. The heuristic algorithm, based on periodic perturbations of the manipulated variable (air-bleed), is validated on a real stack, revealing a stabilized performance without the need of detailed stack properties knowledge.

Structure of Li5AlS4 and comparison with other lithium-containing metal sulfides

NASA Astrophysics Data System (ADS)

Lim, Hanjin; Kim, Sung-Chul; Kim, Jaegyeom; Kim, Young-Il; Kim, Seung-Joo

2018-01-01

Lithium aluminum sulfide (Li5AlS4) was synthesized by solid state reaction, and its crystal structure was characterized by ab initio structure determination on the basis of powder neutron diffraction (ND) data. Li5AlS4 was found to have monoclinic unit cell (space group, P21/m) with the lattice parameters: a = 6.8583(4) Å, b = 7.8369(4) Å, c = 6.2488(4) Å, and β = 90.333(4)°. This structure is built from a hexagonal close-packed (hcp) arrangement of sulfur atoms with a stacking sequence of …ABAB…. The hcp sulfide lattice consists of two different double-sulfide layers alternately stacked along the c-axis. Between the first pair of sulfur layers all the tetrahedral interstices (T+ and T- sites) are filled with lithium and aluminum atoms. All octahedral interstices between the second pair of sulfur layers are occupied by the remaining lithium atoms. The structure of Li5AlS4 is compared with those of various lithium-containing metal sulfides like Li2FeS2, NaLiMS2 (M = Zn, Cd), Li4GeS4, LiM‧S2 (M‧ = Al, Ga, In) and γ-Li3PS4. Each sulfide represents a specific distribution of lithium atoms in the lattice depending on how the octahedral and tetrahedral interstitial sites are filled. The low ionic conductivity of Li5AlS4 (9.7 × 10-9 S cm-1 at 323 K) relative to other sulfides may be due to the highly-ordered distribution of the lithium atoms in the layered structure and the lack of adjacent void spaces that can be used for lithium ion hopping.

Higher-order molecular packing in amyloid-like fibrils constructed with linear arrangements of hydrophobic and hydrogen-bonding side-chains.

PubMed

Saiki, Masatoshi; Honda, Shinya; Kawasaki, Kazunori; Zhou, Deshan; Kaito, Akira; Konakahara, Takeo; Morii, Hisayuki

2005-05-13

Various mutants of the protein fragment, barnase module-1 (1-24) were investigated in order to reveal the structural principle of amyloid-like fibrils. By means of circular dichroism spectroscopy, X-ray diffraction, electron microscopy, and thioflavin T binding assay, we found that the molecules containing two beta-strands and an intervening turn structure are assembled to form a cross-beta structure. Stabilization by both the hydrophobic interactions and hydrogen bonding between the respective paired side-chains on the coupled beta-strands was essential for fibril formation. These two types of interaction can also arrange the corresponding residues in lines on both sheet surfaces of protofilaments with a cross-beta structure. This leads to the most probable fibril structure constructed with the line-matching interactions between protofilaments. Consideration of the geometrical symmetry resulted in our finding that a limited number of essential models for molecular packing in fibril structure are stable, which would rationally explain the occurrence of two or three morphologies from an identical molecular species. The ribbon-like fibrils exhibited striped texture along the axis, which was assigned to a stacked two-sheet repeat as a structural unit. The comprehensively proposed structural model, that is, the sheet-sheet interaction between left-handed cross-beta structures, results in a slightly right-handed twist of beta-sheet stacking, which reasonably elucidates the intrinsic sizes of the fibril width and its helical period along the fibril axis, as the bias in the orientation of the hydrogen-bonded beta-strand pair at the lateral edge is larger than that at the central protofilament.

Gel electrophoretic isolation, in the hundred microgram range, of recombinant SDS-syntaxin from sea urchin egg cortical vesicles.

PubMed

Li, Y M; Chrambach, A

2001-11-01

Recombinant urchin syntaxin [Xa cut], electrophoresed at pH 9.0 (25 degrees C) or 10.2 (0 degrees C) in a discontinuous Tris-chloride-glycinate buffer system in the presence of 0.03% SDS in the catholyte, exhibits a multicomponent pattern in gels of a polyacrylamide concentration of 12% and 3% crosslinking. The position in the pattern of the syntaxin band was identified by reference to electropherograms of a previous study (P. Backlund, pers. comm.). The complexity of the protein composition of the preparation was reduced by selective stacking of proteins with mobilities greater than that of syntaxin. This provides a gel pattern consisting of two bands with mobilities close to that identified as syntaxin, as well as a minor, more slowly migrating, contaminant. The two major components are designated as S1 and S2, the latter being the larger species. In the absence of SDS, the preparation exhibits two pairs of protein components. Three of the proteins are charge isomers, i.e., of equal size, differing only in net charge, assumed to be forms of S1, while the fourth component is larger and is assumed to be S2. Aliquots of the preparation, containing 150 microg of protein were loaded on a cylindrical polyacrylamide gel of 18 mm diameter, and separated S1 and S2 were excised in a position defined by their characteristic values of relative mobility (Rf). Two or three gel slices, corresponding in Rf to S1 or S2, were pooled and loaded onto a Stacking Gel (5% polyacrylamide, 20% cross-linked) of 18 mm diameter, equipped with a collection chamber of 200 microL volume. The protein was electroeluted from the gel slices and concentrated into a stack by electrophoresis. The stack, marked by bromphenolblue, was allowed to migrate into the collection chamber, was collected and analyzed by protein assay and re-electrophoresis. Re-electrophoresis of S1 shows that it consists of at least three components. Recovered S1 constitutes 47% of the preparation, based on protein assay, S2 4%. S1, isolated from SDS-PAGE, exhibits an apparent Mr of 22.7 kDa, S2 one of 34.5 kDa, similar to the value of 32.6 kDa expected from the structure of syntaxin. The absence of S2 from the electroeluate re-electrophoresed at 0 degrees C and their molecular weight relationship suggest a proteolytic transformation of S2 to S1.