Browsing by Subject "Structure analysis"

Now showing 1 - 8 of 8

Open Access
The BioPAX community standard for pathway data sharing
(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.
Open Access
Electronic excited states of the CP29 antenna complex of green plants: a model based on exciton calculations
(Springer / Kluwer Academic Publishers, 2000) İşerı, E. İ.; Albayrak, D.; Gülen, D.
We have suggested a model for the electronic excited states of the minor plant antenna, CP29, by incorporating a considerable part of the current information offered by structure determination, site-directed mutagenesis, and spectroscopy in the modeling. We have assumed that the electronic excited states of the complex have been decided by the chlorophyll-chlorophyll (Chl) and Chl-protein interactions and have modeled the Coulombic interaction between a pair of Chls in the point-dipole approximation and the Chl-protein interactions are treated as empirical fit parameters. We have suggested the Qy dipole moment orientations and the site energies for all the chlorophylls in the complex through a simultaneous simulation of the absorption and linear dichroism spectra. The assignments proposed have been discussed to yield a satisfactory reproduction of all prominent features of the absorption, linear and circular dichroism spectra as well as the key spectral and temporal characteristics of the energy transfer processes among the chlorophylls. The orientations and the spectral assignments obtained by relatively simple exciton calculations have been necessary to provide a good point of departure for more detailed treatments of structure-function relationship in CP29. Moreover, it has been discussed that the CP29 model suggested can guide the studies for a better understanding of the structure-function relationship in the major plant antenna, LHCII.
Open Access
Guiding, bending, and splitting of electromagnetic waves in highly confined photonic crystal waveguides
(American Physical Society, 2001) Bayındır, Mehmet; Özbay, Ekmel; Temelkuran, B.; Sigalas, M. M.; Soukoulis, C. M.; Biswas, R.; Ho, K. M.
We have experimentally demonstrated the guiding, bending, and splitting of electromagnetic (EM) waves in highly confined waveguides built around three-dimensional layer-by-layer photonic crystals by removing a single rod. Full transmission of the EM waves was observed for straight and bended waveguides. We also investigated the power splitter structures in which the input EM power could be efficiently divided into the output waveguide ports. The experimental results, dispersion relation and photon lifetime, were analyzed with a theory based on the tight-binding photon picture. Our results provide an important tool for designing photonic crystal based optoelectronic components.
Open Access
Metal nanoring and tube formation on carbon nanotubes
(American Physical Society, 2002) Bagci, V. M. K.; Gülseren, O.; Yildirim, T.; Gedik, Z.; Ciracil, S.
The structural and electronic properties of aluminum-covered single-wall carbon nanotubes (SWNT's) are studied from first principles for a large number of coverages. Aluminum-aluminum interaction, that is stronger than aluminum-tube interaction, prevents uniform metal coverage, and hence gives rise to the clustering. However, a stable aluminum ring and aluminum nanotube with well defined patterns can also form around the semiconducting SWNT's and lead to metallization. The persistent current in the Al nanoring is discussed to show that a high magnetic field can be induced at the center of SWNT.
Open Access
Oxygenation of carbon nanotubes: Atomic structure, energetics, and electronic structure
(American Physical Society, 2003) Dag, S.; Gülseren, O.; Yildirim, T.; Çıracı, Salim
This paper presents an extensive and systematic analysis of the oxygenation of semiconducting and metallic single-wall carbon nanotubes by using the first principles pseudopotential plane wave method. Our study involves the physisorption of oxygen molecules, chemisorption of oxygen atoms and formation of an oxide, and deals with the equilibrium binding geometry and corresponding electronic energy structure. The binding energies of an oxygen molecule physisorbed at different sites are determined by calculating short and long range interactions. The triplet state of the physisorbed oxygen molecule is energetically favorable, whereas the nonmagnetic (spin paired) state yields a relatively stronger binding energy. An oxygen atom is adsorbed on top of the carbon-carbon bond. The zigzag bonds of the nanotubes are weakened and eventually are replaced by a carbon-oxygen-carbon bridge bond. Chemisorption of atomic oxygen and physisorption of an oxygen molecule modify the electronic energy structure of the bare tube in different ways. For a different coverage and pattern, self-consistent field electronic energy structure calculations using the optimized physisorption geometry corresponding to the triplet ground state result in a small energy gap between unoccupied oxygen levels and the top of the valence band of the semiconducting carbon nanotube. These results invalidate the hole doping of the semiconducting carbon nanotube upon the physisorption of oxygen.
Open Access
Poly-cyclodextrin cryogels with aligned porous structure for removal of polycyclic aromatic hydrocarbons (PAHs) from water
(Elsevier, 2017-08) Topuz, F.; Uyar, Tamer
Cyclodextrins (CDs) are sugar-based cyclic oligosaccharides, which form inclusion complexes with small guest molecules through their hydrophobic cavity. Here we successfully synthesized highly porous poly-cyclodextrin (poly-CD) cryogels, which were produced under cryogenic conditions by the cross-linking of amine-functional CDs with PEG-based diepoxide cross-linker. The poly-CD cryogels showed aligned porous network structures owing to the directional freezing of the matrix, of which the pore size and architecture exposed variations depending on the composition of the reactants. The cryogels were employed for the removal of genotoxic polycyclic aromatic hydrocarbons (PAHs) from aqueous solutions. They reached PAH sorption capacities as high as 1.25 mg PAH per gram cryogel. This high sorption performance is due to interactions between PAHs and the complete swollen network, and thus, is not restricted by interfacial adsorption. Given that the hydrophilic nature of the components, the sorption performance could only be attributed to the inclusion complex formation of CDs with PAH molecules. The poly-CD cryogels could be recycled with an exposure to ethanol and reused without any significant loss in the sorption capacity of PAHs.
Open Access
Pyramidalized double bonds containing endoperoxide linkages: photooxygenation of dimethyl cis-3,8-dihydroheptalene-3,8, dicarboxylate
(American Chemical Society, 1999) Saraçoǧlu, N.; Menzek, A.; Sayan, Ş.; Salzner, U.; Balci, M.
Diels-Alder cycloaddition utilizing singlet oxygen as the dienophile with dimethyl cis-3,8-dihydroheptalene-3,8-dicarboxylate (5) has been investigated, and monoaddition product 7 has been isolated. The addition of a second singlet oxygen to the cycloheptatriene unit in 7 gave syn- bis(norcaradiene) bis(endoperoxide) 4. 1H NMR spectral studies and theoretical calculations indicate the increased pyramidalization in syn-4 compared with carbon analogue. The increased pyramidalization results from hyperconjugation between the central π-bond and the four adjacent C-O bonds and by rehybridization at C3, C4, C5, and C6. Furthermore, the increased reactivity for syn-4, which is probably arising from further folding of the central double bond, is also in agreement with theoretical calculations.
Open Access
Theoretical study of crossed and parallel carbon nanotube junctions and three-dimensional grid structures
(American Physical Society, 2004) Dag, S.; Senger, R. T.; Çıracı, Salim
This work presents a first-principles study of parallel and crossed junctions of single-wall carbon nanotubes (SWNT). The crossed junctions are modeled by two-dimensional grids of zigzag SWNTs. The atomic and electronic structure, stability, and energetics of the junctions are studied for different magnitudes of contact forces pressing the tubes towards each other and hence inducing radial deformations. Under relatively weak contact forces the tubes are linked with intertube bonds which allow a significant conductance through the junction. These interlinking bonds survive even after the contact forces are released and whole structure is fully relaxed. Upon increasing contact force and radial deformation the tube surfaces are flattened but the interlinking bonds are broken to lead to a relatively wider intertube spacing. The intertube conductance through such a junction diminish because of finite potential barrier intervening between the tubes. The linkage of crossing tubes to form stable junctions is enhanced by a vacancy created at the contact. The three-dimensional grid structure formed by SWNTs is also investigated as a possible framework in device integration.