Browsing by Subject "Molecular interaction"

Now showing 1 - 16 of 16

Open Access
Atomic scale study of superlow friction between hydrogenated diamond surfaces
(American Physical Society, 2004) Dag, S.; Çıracı, Salim
Strong attractive interaction between two clean diamond (001) slabs turns repulsive upon the hydrogenation of surfaces. This repulsive interaction serves as if a boundary lubricant and prevents the sliding surfaces from being closer to each other even under high normal forces. As a result, calculated lateral force variation generated during sliding has small magnitude under high constant loading forces. Superlow friction observed earlier between diamondlike carbon-coated surfaces can be understood by the steady repulsive interaction between sliding surfaces, as well as strong and stiff carbon-carbon and carbon-hydrogen bonds which do not favor energy dissipation. In ambient conditions, the steady repulsive interaction is, however, destroyed by oxygen atoms which chemically modify those stiff surface bonds.
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
Dispersion of multi-walled carbon nanotubes in an aqueous medium by water-dispersible conjugated polymer nanoparticles
(2010) Baykal, B.; Ibrahimova, V.; Er, G.; Bengü, E.; Tuncel, D.
Vertically aligned multi-walled carbon nanotubes (MWCNTs) synthesized by the alcohol catalytic CVD (ACCVD) technique are dispersed in water with the aid of water-dispersible conjugated polymer nanoparticles (CPNs). The interactions between CPNs and CNTs are studied with spectroscopy (UV-Vis, fluorescence and Raman) and electron microscopy techniques are used to confirm attachment of CPNs to the CNT sidewalls.
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
FTIR studies of vitamin E-cholesterol-DPPC membrane interactions in CH2 region
(Springer-Verlag, 1996) Severcan, F.; Baykal, Ü.; Süzer, Ş.
Binary and ternary mixtures of α-tocopherol (αT), cholesterol and dipalmitoyl phosphatidylcholine (DPPC) in the form of multilamellar liposomes have been investigated by Fourier Transform Infrared Spectroscopy (FTIR). Investigation of frequencies, bandwidths and band shapes of CH2 stretching and scissoring bands indicate that the effect of αT is dominant in comparison with cholesterol and αT decreases the interaction of cholesterol with phospholipid membranes. © Springer-Verlag 1996.
Open Access
Highly sensitive determination of 2, 4, 6-trinitrotoluene and related byproducts using a diol functionalized column for high performance liquid chromatography
(Public Library of Science, 2014) Gumuscu, B.; Erdogan, Z.; Güler, Mustafa O.; Tekinay, T.
In this work, a new detection method for complete separation of 2,4,6-trinitrotoluene (TNT); 2,4-dinitrotoluene (2,4-DNT); 2,6-dinitrotoluene (2,6-DNT); 2-aminodinitrotoluene (2-ADNT) and 4-aminodinitrotoluene (4-ADNT) molecules in high-performance liquid-chromatography (HPLC) with UV sensor has been developed using diol column. This approach improves on cost, time, and sensitivity over the existing methods, providing a simple and effective alternative. Total analysis time was less than 13 minutes including column re-equilibration between runs, in which water and acetonitrile were used as gradient elution solvents. Under optimized conditions, the minimum resolution between 2,4-DNT and 2,6-DNT peaks was 2.06. The recovery rates for spiked environmental samples were between 95-98%. The detection limits for diol column ranged from 0.78 to 1.17 μg/L for TNT and its byproducts. While the solvent consumption was 26.4 mL/min for two-phase EPA and 30 mL/min for EPA 8330 methods, it was only 8.8 mL/min for diol column. The resolution was improved up to 49% respect to two-phase EPA and EPA 8330 methods. When compared to C-18 and phenyl-3 columns, solvent usage was reduced up to 64% using diol column and resolution was enhanced approximately two-fold. The sensitivity of diol column was afforded by the hydroxyl groups on polyol layer, joining the formation of charge-transfer complexes with nitroaromatic compounds according to acceptor-donor interactions. Having compliance with current requirements, the proposed method demonstrates sensitive and robust separation. © 2014 Gumuscu et al.
Open Access
Hydrogenation of naphthalene and methylnaphthalene: modeling and spectroscopy
(Elsevier BV, 2002) Sayan, Ş.; Paul, J.
In situ infrared spectra of 1-methylnaphthalene (1-MeNapht)hydrogenation, over sulfided NiMo/Al2O3-TiO2 catalysts, were compared with theoretically derived properties of methylnaphthalene and its bicyclic products: MeDilin, MeTetralin, MeOctalin and MeDecalin, and with conversion data from literature. Comparisons were also made between the un-substituted and methyl-substituted two-rings, and between the 1- and 5-methyl isomers of 1,4-dihydronaphthalene (dilin) and 1,2,3,4-tetrahydronaphthalene (tetralin). IR spectra of MeNapht adsorption, on the sulfided catalyst, were matched with data for adsorption on the catalyst without sulfidation and the empty support. Surface bound MeNapht is observed below 250°C on all catalysts. MeNapht adsorption suppresses OH groups nondiscriminatory on the empty support and the metal loaded catalyst. We relate the results to previous data on the interaction between the supported metal sulfides and titanium modified aluminas. Calculated total energies, and experimentally derived heats of formation, pointed at decahydronaphthalene (decalin) as the dominant product of naphthalene hydrogenation, with tetralin as an abundant intermediate, and dilin and 1,2,3,4,5,6,7,8-octahydronaphthalene (octalin) as short lived transient stages. The spectroscopic modeling showed that the orbital fingerprints of the five bicyclic compounds were not distinctly different, nor more than marginally modified by methyl substitution or isomerization. The only significant difference came at the highest occupied orbital, where a high naphthalene density of states (DoS) overlapped with the valence bands of metal or metal sulfide catalysts. The vibrational bands for naphthalene, dilin, tetralin and octalin were well separated. Octalin and decalin, alone, have similar vibrational spectra. Upheaval of ring degeneracy for methyl-substituted two-ring structures broadened all infrared bands in a characteristic way.
Open Access
Manipulation of atoms across a surface at room temperature
(Nature Publishing Group, 2000) Fishlock, T. W.; Oral, A.; Egdell, R. G.; Pethica, J. B.
Since the realization that the tips of scanning probe microscopes can interact with atoms at surfaces, there has been much interest in the possibility of building or modifying nanostructures or molecules directly from single atoms. Individual large molecules can be positioned on surfaces, and atoms can be transferred controllably between the sample and probe tip. The most complex structures are produced at cryogenic temperatures by sliding atoms across a surface to chosen sites. But there are problems in manipulating atoms laterally at higher temperatures - atoms that are sufficiently well bound to a surface to be stable at higher temperatures require a stronger tip interaction to be moved. This situation differs significantly from the idealized weakly interacting tips of scanning tunnelling or atomic force microscopes. Here we demonstrate that precise positioning of atoms on a copper surface is possible at room temperature. The triggering mechanism for the atomic motion unexpectedly depends on the tunnelling current density, rather than the electric field or proximity of tip and surface.
Open Access
Multivalent presentation of cationic peptides on supramolecular nanofibers for antimicrobial activity
(American Chemical Society, 2017) Beter, M.; Kara, H. K.; Topal, A. E.; Dana, A.; Tekinay, A. B.; Güler, Mustafa O.
Noncovalent and electrostatic interactions facilitate the formation of complex networks through molecular self-assembly in biomolecules such as proteins and glycosaminoglycans. Self-assembling peptide amphiphiles (PA) are a group of molecules that can form nanofibrous structures and may contain bioactive epitopes to interact specifically with target molecules. Here, we report the presentation of cationic peptide sequences on supramolecular nanofibers formed by self-assembling peptide amphiphiles for cooperative enhanced antibacterial activity. Antibacterial properties of self-assembled peptide nanofibers were significantly higher than soluble peptide molecules with identical amino acid sequences, suggesting that the tandem presentation of bioactive epitopes is important for designing new materials for bactericidal activity. In addition, bacteria were observed to accumulate more rapidly on peptide nanofibers compared to soluble peptides, which may further enhance antibacterial activity by increasing the number of peptide molecules interacting with the bacterial membrane. The cationic peptide amphiphile nanofibers were observed to attach to bacterial membranes and disrupt their integrity. These results demonstrate that short cationic peptides show a significant improvement in antibacterial activity when presented in the nanofiber form.
Open Access
An ontology for collaborative construction and analysis of cellular pathways
(Oxford University Press, 2004-02-12) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül
Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology. © Oxford University Press 2004; All rights reserved.
Open Access
Orbital magnetization of single and double quantum dots in a tight-binding model
(American Physical Society, 2003) Aldea, A.; Moldoveanu, V.; Niţǎ, M.; Manolescu, A.; Gudmundsson, V.; Tanatar, Bilal
We calculate the orbital magnetization of single and double quantum dots coupled both by Coulomb interaction and by electron tunneling. The electronic states of the quantum dots are calculated in a tight-binding model, and the magnetization is discussed in relation to the energy spectrum and to the edge and bulk states. We identify effects of chirality of the electronic orbits and of the anticrossing of the energy levels when the magnetic field is varied. We also consider the effects of detuning the energy spectra of the quantum dots by an external gate potential. We compare our results with the recent experiments of Oosterkamp et al. [Phys, Rev. Lett. 80, 4951 (1998)].
Open Access
PATIKAmad: putting microarray data into pathway context
(Wiley - V C H Verlag GmbH & Co. KGaA, 2008-06) Babur, Özgün; Colak, Recep; Demir, Emek; Doğrusöz, Uğur
High-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's proteome. Studies and tools with this purpose are limited to networks with simple structure, such as protein-protein interaction graphs, or do not go much beyond than simply displaying values on the network. We have built a microarray data analysis tool, named PATIKAmad, which can be used to associate microarray data with the pathway models in mechanistic detail, and provides facilities for visualization, clustering, querying, and navigation of biological graphs related with loaded microarray experiments. PATIKAmad is freely available to noncommercial users as a new module of PATIKAweb at http://web.patika.org. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.
Open Access
Power dissipation analysis in tapping-mode atomic force microscopy
(American Physical Society, 2003) Balantekin, M.; Atalar, Abdullah
In a tapping-mode atomic force microscope, a power is dissipated in the sample during the imaging process. While the vibrating tip taps on the sample surface, some part of its energy is coupled to the sample. Too much dissipated power may mean the damage of the sample or the tip. The amount of power dissipation is related to the mechanical properties of a sample such as viscosity and elasticity. In this paper, we first formulate the steady-state tip-sample interaction force by a simple analytical expression, and then we derive the expressions for average and maximum power dissipated in the sample by means of sample parameters. Furthermore, for a given sample elastic properties we can determine approximately the sample damping constant by measuring the average power dissipation. Simulation results are in close agreement with our analytical approach.
Open Access
Site-specific fluorescence polarization for studying the disaggregation of α-synuclein fibrils by small molecules
(American Chemical Society, 2017) Haney, C. M.; Cleveland, C. L.; Wissner, R. F.; Owei, L.; Robustelli, J.; Daniels, M. J.; Canyurt, M.; Rodriguez, P.; Ischiropoulos, H.; Baumgart, T.; Petersson, E. J.
Fibrillar aggregates of the protein α-synuclein (αS) are one of the hallmarks of Parkinson’s disease. Here, we show that measuring the fluorescence polarization (FP) of labels at several sites on αS allows one to monitor changes in the local dynamics of the protein after binding to micelles or vesicles, and during fibril formation. Most significantly, these site-specific FP measurements provide insight into structural remodeling of αS fibrils by small molecules and have the potential for use in moderate-throughput screens to identify small molecules that could be used to treat Parkinson’s disease. © 2016 American Chemical Society.
Open Access
Spin magnetization of a strongly correlated electron gas confined in a two-dimensional finite lattice
(American Physical Society, 2004) Niţǎ, M.; Dinu, V.; Aldea, A.; Tanatar, Bilal
The influence of disorder and interaction effects on the ground state polarization of the two-dimensional correlated electron gas is studied by numerical investigations of the unrestricted Hartree-Fock approach. With the model of Anderson disorder a continuous increase of the spin magnetization until the fully polarized regime is obtained. The ferromagnetic ground state is found to be favorable when the electron number is lowered and the interaction and disorder parameters are suitably chosen.
Open Access
Tunneling properties of quantum dot arrays in a strong magnetic field
(The American Physical Society, 2004) Moldoveanu, V.; Aldea, A.; Tanatar, Bilal
We study the transport properties of coherently coupled quantum dots in the quantum Hall regime within the Landauer-Büttiker formalism which captures and explains the experimentally observed features in terms of the spectral properties of the coupled dot system. The subpeak structure of the transmittance spectrum and the charging stability diagrams are obtained and discussed. The role of the intradot and interdot Coulomb interaction are pointed out. We show the subpeak evolution with the magnetic field and predict a specific oscillatory behavior of the Hall resistance in strong magnetic field which can be experimentally tested.