Browsing by Keywords "Molecular dynamics"

Now showing items 1-20 of 24

    • Ab initio temperature dependent studies of the homoepitaxial growth on Si(0 0 1) surface 

      Dağ, S.; Çıracı, Salim; Kılıç, Ç.; Fong, C. Y. (2001)
      We performed ab initio zero temperature and finite temperature molecular dynamics calculations to investigate the homoepitaxial growth on the Si(0 0 1) surface. How do the deposited atoms (adatoms) form addimers and how ...

    • Atomic strings of group IV, III-V, and II-VI elements 

      Tongay, S.; Durgun, Engin; Çıracı, Salim (American Institute of Physics, 2004)
      A systematic first-principles study of atomic strings made by group IV, III-V, and II-VI elements has revealed interesting mechanical, electronic, and transport properties. The double bond structure underlies their unusual ...

    • The BioPAX community standard for pathway data sharing 

      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. (Nature Publishing Group, 2010-09)
      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 ...

    • Chiral ceramic nanoparticles and peptide catalysis 

      Jiang S.; Chekini, M.; Qu, Z.-B.; Wang Y.; Yeltik A.; Liu, Y.; Kotlyar, A.; Zhang, T.; Li, B.; Demir, Hilmi Volkan; Kotov, N. A. (American Chemical Society, 2017)
      The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in nature. The ...

    • Development of force fields for novel 2D materials for temperature dependent vibrational properties 

      Mobaraki, Arash (Bilkent University, 2019-09)
      A new era of nanodevice engineering has been started after fabricating graphene. This motivated vast number of researches for predicting, fabricating and utilizing 2D materials. Temperature dependent properties are ...

    • Dynamic correlation effects on the plasmon dispersion in a two-dimensional electron gas 

      Yurtsever, A.; Moldoveanu, V.; Tanatar, Bilal (The American Physical Society, 2003)
      The charge-density oscillations (plasmons) of a low-density two-dimensional uniform electron gas are studied within the framework of finite temperature and frequency dependent (dynamic) version of Singwi, Tosi, Land, and ...

    • Dynamic correlations in double-layer electron systems 

      Tanatar, Bilal; Davoudi, B. (The American Physical Society, 2001)
      We study the effects of dynamic correlations on the ground-state properties of a double-layer two-dimensional electron gas within the quantum Singwi-Tosi-Land-Sjölander theory (STLS). The intralayer and interlayer static ...

    • Effects of temperature, pH and counterions on the stability of peptide amphiphile nanofiber structures 

      Ozkan A.D.; Tekinay, A. B.; Güler, Mustafa O.; Tekin, E. D. (Royal Society of Chemistry, 2016)
      Peptide amphiphiles are a class of self-assembling molecules that are widely used to form bioactive nanostructures for various applications in bionanomedicine. However, peptide molecules can exhibit distinct behaviors under ...

    • Fast multipole methods in service of various scientific disciplines 

      Gürel, Levent (IEEE, 2014)
      For more than two decades, several forms of fast multipole methods have been extremely successful in various scientific disciplines. Reduced complexity solutions are obtained for solving different forms of equations that ...

    • Finite temperature studies of Te adsorption on Si(0 0 1) 

      Sen, P.; Çıracı, Salim; Batra, I. P.; Grein, C. H.; Sivananthan, S. (Elsevier, 2002)
      We perform first principles density functional calculations to investigate the adsorption of Te on the Si(0 0 1) surface from low coverage up to a monolayer coverage. At low coverage, a Te atom is adsorbed on top of the ...

    • Hierarchical self-assembly of histidine-functionalized peptide amphiphiles into supramolecular chiral nanostructures 

      Koc, M. H.; Ciftci, G. C.; Baday, S.; Castelletto, V.; Hamley, I. W.; Güler, Mustafa O. (American Chemical Society, 2017)
      Controlling the hierarchical organization of self-assembling peptide amphiphiles into supramolecular nanostructures opens up the possibility of developing biocompatible functional supramolecular materials for various ...

    • A highly sensitive atomic force microscope for linear measurements of molecular forces in liquids 

      Patil, S.; Matei, G.; Dong, H.; Hoffmann, P. M.; Karaköse, M.; Oral, A. (American Institute of Physics, 2005)
      We describe a highly improved atomic force microscope for quantitative nanomechanical measurements in liquids. The main feature of this microscope is a modified fiber interferometer mounted on a five axis inertial slider ...

    • Hydrogen storage capacity of titanium met-cars 

      Akman, N.; Durgun, Engin; Yildirim, T.; Çıracı, Salim (IOP Publishing Ltd., 2006)
      The adsorption of hydrogen molecules on the titanium metallocarbohedryne (met-car) cluster has been investigated by using the first-principles plane wave method. We have found that, while a single Ti atom at the corner can ...

    • Insight on tricalcium silicate hydration and dissolution mechanism from molecular simulations 

      Manzano, H.; Durgun, Engin; Arbeloa, I. L.; Grossman, J. C. (American Chemical Society, 2015)
      Hydration of mineral surfaces, a critical process for many technological applications, encompasses multiple coupled chemical reactions and topological changes, challenging both experimental characterization and computational ...

    • Interactions between densely grafted molten polymer brushes: scaling theories versus molecular simulations 

      Erbaş, Aykut (Scientific and Technical Research Council of Turkey - TUBITAK,Turkiye Bilimsel ve Teknik Arastirma Kurumu, 2021-02-27)
      Using molecular dynamics simulations and scaling arguments, we analyzed the interactions between two identical molten polymer brushes intermediately and strongly compressed towards each other at melt conditions. The width ...

    • Manipulation of atoms across a surface at room temperature 

      Fishlock, T. W.; Oral, A.; Egdell, R. G.; Pethica, J. B. (Nature Publishing Group, 2000)
      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 ...

    • Molecular dynamics simulations study of [5]rotaxane in bulk and at interfaces 

      Özkan, Ata Utku (Bilkent University, 2022-06)
      Rotaxanes are a class mechanically interlocked molecular architectures that exhibit quasi-mechanical movement in response to specific stimuli. [5]Rotaxane is a complex rotaxane structure that is reported to show extraordinary ...

    • Phase boundary of the boson Mott insulator in a rotating optical lattice 

      Umucalilar, R. O.; Oktel, M. Ö. (The American Physical Society, 2007)
      We consider the Bose-Hubbard model in a two-dimensional rotating optical lattice and investigate the consequences of the effective magnetic field created by rotation. Using a Gutzwiller-type variational wave function, we ...

    • Quantum effects in electrical and thermal transport through nanowires 

      Çıracı, Salim; Buldum, A.; Batra, I. P. (Institute of Physics Publishing, 2001)
      Nanowires, point contacts and metallic single-wall carbon nanotubes are one-dimensional nanostructures which display important size-dependent quantum effects. Quantization due to the transverse confinement and resultant ...

    • Synthesis, anticancer activities and molecular modeling studies of novel indole retinoid derivatives 

      Gurkan-Alp, A. S.; Mumcuoglu, M.; Andac, C. A.; Dayanc, E.; Cetin Atalay, R.; Buyukbingol, E. (Elsevier, 2012)
      In this study, novel (E)-3-(5-substituted-1H-indol-3-yl)-1-(5,5,8,8- tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)prop-2-en-1-one (5(a-e)) derivatives were synthesized and their anticancer effects were determined in vitro. ...