Browsing by Subject "Molecular dynamics"

Now showing items 21-40 of 40

    • Article  

      Further transformation properties of generalised inhomogeneous nonlinear diffusion equations with variable coefficients 

      Sophocleous, Christodoulos (2005)
      We consider the variable coefficient inhomogeneous nonlinear diffusion equations of the form xput = [xqu nux]x. We present further transformation properties for this nonlinear class of equations that do not appear in the ...
    • Article  

      Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulations 

      Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)
      Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...
    • Article  

      Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulationsAAA 

      Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)
      Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...
    • Article  

      InAs quantum dots grown by molecular beam epitaxy on GaAs (211)B polar substrates 

      Zervos, Matthew; Xenogianni, C.; Deligeorgis, G.; Androulidaki, M.; Savvidis, P. G.; Hatzopoulos, Z.; Pelekanos, N. T. (2006)
      InAs nanostructures were grown by molecular beam epitaxy on GaAs (211)B at temperatures between 400-530 °C and growth rates that were varied between 0.1 to 0.02 mono-layers (ML) per second. For temperatures up to 500 °C ...
    • Article  

      Influence of water model and nanotube rigidity on the density of water in carbon nanotubes 

      Alexiadis, A.; Kassinos, Stavros C. (2008)
      The density of water calculated through molecular dynamic simulations using different water models and rigid/flexible carbon nanotubes is studied. A previous equation, determined in an earlier work in order to correlate ...
    • Article  

      Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking 

      Tamamis, Phanourios; Kieslich, C. A.; Nikiforovich, G. V.; Woodruff, T. M.; Morikis, D.; Archontis, Georgios Z. (2014)
      Background: The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence ...
    • Article  

      Liquid expanded monolayers of lipids as model systems to understand the anionic hofmeister series: 2. Ion partitioning is mostly a matter of size 

      Leontidis, Epameinondas; Aroti, Andria (2009)
      In the preceding paper of this series [Leontidis, E.
    • Article  

      Molecular dynamic simulations of carbon nanotubes in CO2 atmosphere 

      Alexiadis, A.; Kassinos, Stavros C. (2008)
      This work investigates by means of molecular dynamics the filling of carbon nanotubes by carbon dioxide molecules. Nanotubes of various sizes are simulated and the resulting CO2 density calculated. The effects of various ...
    • Article  

      Molecular simulation of water in carbon nanotubes 

      Alexiadis, A.; Kassinos, Stavros C. (2008)
      The motion of water in carbon nanotubes (CNT) by numerical procedures is calculated through molecular dynamics (MD) simulation studies. The Lennard-Jones potential is a simple MD simulations technique, which combines ...
    • Article  

      Normal and defective perylene substitution sites in alkane crystals 

      Leontidis, Epameinondas; Heinz, H.; Palewska, K.; Wallenborn, E. -U; Suter, U. W. (2001)
      The substitution nature of perylene in polycrystalline solid alkane matrices was examined. Low temperature excitation-emission matrix spectroscopy was used to determine substitution sites in alkane matrices from hexane to ...
    • Article  

      Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures 

      Gorham, R. D.; Forest, D. L.; Tamamis, Phanourios; López de Victoria, A.; Kraszni, M.; Kieslich, C. A.; Banna, C. D.; Bellows-Peterson, M. L.; Larive, C. K.; Floudas, C. A.; Archontis, Georgios Z.; Johnson, L. V.; Morikis, D. (2013)
      We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide ...
    • Conference Object  

      Particle simulation of crystal growth and settling under variable gravity 

      Gatsonis, N. A.; Ongewe, B.; Alexandrou, Andreas N.; Jr, A. Sacco (American Institute of Aeronautics and Astronautics Inc, AIAA, 1999)
      A model that describes crystal growth and motion is presented. The model is based on concept of the direct simulation Monte Carlo and molecular dynamics methods and includes spherical crystal particles, nutrients species ...
    • Article  

      Search for the supersymmetric partner of the top quark in dilepton events from pp̄ collisions at √s = 1.8 TeV 

      Acosta, D.; Affolder, T.; Akimoto, H.; Albrow, M. G.; Ambrose, D.; Amidei, D.; Anikeev, K.; Antos, J.; Apollinari, G.; Arisawa, T.; Artikov, A.; Asakawa, T.; Ashmanskas, W.; Azfar, F.; Azzi-Bacchetta, P.; Bacchetta, N.; Bachacou, H.; Badgett, W.; Bailey, S.; de Barbaro, P.; Barbaro-Galtieri, A.; Barnes, V. E.; Barnett, B. A.; Baroiant, S.; Barone, M.; Bauer, G.; Bedeschi, F.; Behari, S.; Belforte, S.; Bell, W. H.; Bellettini, G.; Bellinger, J.; Benjamin, D.; Bensinger, J.; Beretvas, Andrew; Berryhill, J.; Bhatti, A.; Binkley, M.; Bisello, D.; Bishai, M.; Blair, R. E.; Blocker, C.; Bloom, K.; Blumenfeld, B.; Blusk, S. R.; Bocci, A.; Bodek, A.; Bolla, G.; Bolshov, A.; Bonushkin, Yu Ye; Bortoletto, D.; Boudreau, J.; Brandl, A.; Bromberg, C.; Brozovic, M.; Brubaker, E.; Bruner, N.; Budagov, J.; Budd, H. S.; Burkett, K.; Busetto, G.; Byrum, K. L.; Cabrera, S.; Calafiura, P.; Campbell, M.; Carithers, W.; Carlson, J.; Carlsmith, D.; Caskey, W.; Castro, A.; Cauz, D.; Cerri, A.; Cerrito, L.; Chan, A. W.; Chang, P. S.; Chang, P. T.; Chapman, J.; Chen, C.; Chen, Y. C.; Cheng, M. -T; Chertok, M.; Chiarelli, G.; Chirikov-Zorin, I.; Chlachidze, G.; Chlebana, F.; Christofek, L.; Chu, M. L.; Chung, J. Y.; Chung, W. H.; Chung, Y. S.; Ciobanu, C. I.; Clark, A. G.; Coca, M.; Colijn, A. P.; Connolly, A.; Convery, M.; Conway, J.; Cordelli, M.; Cranshaw, J.; Culbertson, R.; Dagenhart, D.; D'Auria, S.; de Cecco, S.; DeJongh, F.; Dell'Agnello, Simone; Dell'Orso, M.; Demers, S.; Demortier, L.; Deninno, M.; de Pedis, D.; Derwent, P. F.; Devlin, T.; Dionisi, Carlo; Dittmann, J. R.; Dominguez, A.; Donati, S.; D'Onofrio, M.; Dorigo, T.; Eddy, N.; Einsweiler, K.; Engels Jr., E.; Erbacher, R.; Errede, D.; Errede, S.; Eusebi, R.; Fan, Q.; Farrington, S.; Feild, R. G.; Fernandez, J. P.; Ferretti, C.; Field, R. D.; Fiori, I.; Flaugher, B.; Flores-Castillo, L. R.; Foster, G. W.; Franklin, M.; Freeman, J.; Friedman, J.; Fukui, Y.; Furic, I.; Galeotti, S.; Gallas, A.; Gallinaro, M.; Gao, T.; Garcia-Sciveres, M.; Garfinkel, A. F.; Gatti, P.; Gay, C.; Gerdes, D. W.; Gerstein, E.; Giagu, S.; Giannetti, P.; Giolo, K.; Giordani, M.; Giromini, P.; Glagolev, V.; Glenzinski, D.; Gold, M.; Goldschmidt, N.; Goldstein, J.; Gomez, G.; Goncharov, M.; Gorelov, I.; Goshaw, A. T.; Gotra, Y.; Goulianos, Konstantin; Green, C.; Gresele, A.; Grim, G.; Grosso-Pilcher, C.; Guenther, M.; Guillian, G.; Guimaraes da Costa, J.; Haas, R. M.; Haber, C.; Hahn, S. R.; Halkiadakis, Eva; Hall, C.; Handa, T.; Handler, R.; Happacher, F.; Hara, K.; Hardman, A. D.; Harris, R. M.; Hartmann, F.; Hatakeyama, K.; Hauser, J.; Heinrich, J.; Heiss, A.; Hennecke, M.; Herndon, M.; Hill, C.; Hocker, A.; Hoffman, K. D.; Hollebeek, R.; Holloway, L.; Hou, S.; Huffman, B. T.; Hughes, R.; Huston, J.; Huth, J.; Ikeda, H.; Issever, C.; Incandela, J.; Introzzi, G.; Iori, M.; Ivanov, A.; Iwai, J.; Iwata, Y.; Iyutin, B.; James, E.; Jones, M.; Joshi, U.; Kambara, H.; Kamon, T.; Kaneko, T.; Kang, J.; Karagoz Unel, M.; Karr, K.; Kartal, S.; Kasha, H.; Kato, Y.; Keaffaber, T. A.; Kelley, K.; Kelly, M.; Kennedy, R. D.; Kephart, R.; Khazins, D.; Kikuchi, T.; Kilminster, B.; Kim, B. J.; Kim, D. H.; Kim, H. S.; Kim, M. J.; Kim, S. B.; Kim, S. H.; Kim, T. H.; Kim, Y. K.; Kirby, M.; Kirk, M.; Kirsch, L.; Klimenko, S.; Koehn, P.; Kondo, K.; Konigsberg, J.; Korn, A.; Korytov, A.; Kotelnikov, K.; Kovács, Eve V.; Kroll, J.; Kruse, M.; Krutelyov, V.; Kuhlmann, S. E.; Kurino, K.; Kuwabara, T.; Kuznetsova, N.; Laasanen, A. T.; Lai, N.; Lami, S.; Lammel, S.; Lancaster, J.; Lannon, K.; Lancaster, M.; Lander, R.; Lath, A.; Latino, G.; LeCompte, T.; Le, Y.; Lee, J.; Lee, S. W.; Leonardo, N.; Leone, S.; Lewis, J. D.; Li, K.; Lin, C. S.; Lindgren, M.; Liss, T. M.; Liu, J. B.; Liu, T.; Liu, Y. C.; Litvintsev, D. O.; Lobban, O.; Lockyer, N. S.; Loginov, A.; Loken, J.; Loreti, M.; Lucchesi, D.; Lukens, P.; Lusin, S.; Lyons, L.; Lys, J.; Madrak, R.; Maeshima, K.; Maksimovic, P.; Malferrari, L.; Mangano, M.; Manca, G.; Mariotti, M.; Martignon, G.; Martin, M.; Martin, A.; Martin, V.; Martinez, M.; Matthews, J. A. J.; Mazzanti, P.; McFarland, K. S.; McIntyre, P.; Menguzzato, M.; Menzione, A.; Merkel, P.; Mesropian, C.; Meyer, A.; Miao, T.; Miller, R.; Miller, J. S.; Minato, H.; Miscetti, S.; Mishina, M.; Mitselmakher, G.; Miyazaki, Y.; Moggi, N.; Moore, E.; Moore, R.; Morita, Y.; Moulik, T.; Mulhearn, M.; Mukherjee, A.; Muller, T.; Munar, A.; Murat, P.; Murgia, S.; Nachtman, J.; Nagaslaev, V.; Nahn, S.; Nakada, H.; Nakano, I.; Napora, R.; Niell, F.; Nelson, C.; Nelson, T.; Neu, C.; Neubauer, M. S.; Neuberger, D.; Newman-Holmes, C.; Ngan, C. -Y P.; Nigmanov, T.; Niu, H.; Nodulman, L.; Nomerotski, A.; Oh, S. H.; Oh, Y. D.; Ohmoto, T.; Ohsugi, T.; Oishi, R.; Okusawa, T.; Olsen, J.; Orejudos, W.; Pagliarone, C.; Palmonari, F.; Paoletti, R.; Papadimitriou, Vaia; Partos, D.; Patrick, J.; Pauletta, G.; Paulini, M.; Pauly, T.; Paus, C.; Pellett, D.; Penzo, A.; Pescara, L.; Phillips, T. J.; Piacentino, G.; Piedra, J.; Pitts, K. T.; Pompoš, A.; Pondrom, L.; Pope, G.; Pratt, T.; Prokoshin, F.; Proudfoot, J.; Ptohos, Fotios; Pukhov, O.; Punzi, G.; Rademacker, J.; Rakitine, A.; Ratnikov, F.; Ray, H.; Reher, D.; Reichold, A.; Renton, P.; Rescigno, M.; Ribon, A.; Riegler, W.; Rimondi, F.; Ristori, L.; Riveline, M.; Robertson, W. J.; Rodrigo, T.; Rolli, S.; Rosenson, L.; Roser, R.; Rossin, R.; Rott, C.; Roy, A.; Ruiz, A.; Ryan, D.; Safonov, A.; St. Denis, R.; Sakumoto, W. K.; Saltzberg, D.; Sanchez, C.; Sansoni, A.; Santi, L.; Sarkar, S.; Sato, H.; Savard, P.; Savoy-Navarro, A.; Schlabach, P.; Schmidt, E. E.; Schmidt, M. P.; Schmitt, M.; Scodellaro, L.; Scott, A.; Scribano, A.; Sedov, A.; Seidel, S.; Seiya, Y.; Semenov, A.; Semeria, F.; Shah, T.; Shapiro, M. D.; Shepard, P. F.; Shibayama, T.; Shimojima, M.; Shochet, M.; Sidoti, A.; Siegrist, J.; Sill, A.; Sinervo, P.; Singh, P.; Slaughter, A. J.; Sliwa, K.; Snider, F. D.; Snihur, R.; Solodsky, A.; Spalding, J.; Speer, T.; Spezziga, M.; Sphicas, Paris A.; Spinella, F.; Spiropulu, Maria; Spiegel, L.; Steele, J.; Stefanini, A.; Strologas, John; Strumia, F.; Stuart, D.; Sukhanov, A.; Sumorok, K.; Suzuki, T.; Takano, T.; Takashima, R.; Takikawa, K.; Tamburello, P.; Tanaka, M.; Tannenbaum, B.; Tecchio, M.; Tesarek, R. J.; Teng, P. K.; Terashi, K.; Tether, S.; Thom, J.; Thompson, A. S.; Thomson, E.; Thurman-Keup, R.; Tipton, P.; Tkaczyk, S.; Toback, D.; Tollefson, K.; Tonelli, D.; Tonnesmann, M.; Toyoda, H.; Trischuk, W.; de Trocóniz, J. F.; Tseng, J.; Tsybychev, D.; Turini, N.; Ukegawa, F.; Unverhau, T.; Vaiciulis, T.; Valls, J.; Varganov, A.; Vataga, E.; Vejcik III, S.; Velev, G.; Veramendi, G.; Vidal, R.; Vila, I.; Vilar, R.; Volobouev, I.; von der Mey, M.; Vucinic, D.; Wagner, R. G.; Wagner, R. L.; Wagner, W.; Wallace, N. B.; Wan, Z.; Wang, C.; Wang, M. J.; Wang, S. M.; Ward, B.; Waschke, S.; Watanabe, T.; Waters, D.; Watts, T.; Weber, M.; Wenzel, H.; Wester III, W. C.; Whitehouse, B.; Wicklund, A. B.; Wicklund, E.; Wilkes, T.; Williams, H. H.; Wilson, P.; Winer, B. L.; Winn, D.; Wolbers, S.; Wolinski, D.; Wolinski, J.; Wolinski, S.; Wolter, M.; Worm, S.; Wu, X.; Würthwein, F.; Wyss, J.; Yang, U. K.; Yao, W.; Yeh, G. P.; Yeh, P.; Yi, K.; Yoh, J.; Yosef, C.; Yoshida, T.; Yu, I.; Yu, S.; Yu, Z.; Yun, J. C.; Zanello, L.; Zanetti, A.; Zetti, F.; Zucchelli, S. (2003)
      The article discussed about the supersymmetric particles of the top quark in Dilepton events. The Collider Detector at Fermilab was used to gather supersymmetry particles. Due to the high mass, stop decays into the top ...
    • Article  

      Self-assembly of an aspartate-rich sequence from the adenovirus fiber shaft: Insights from molecular dynamics simulations and experiments 

      Tamamis, Phanourios; Terzaki, K.; Kassinopoulos, Marios; Mastrogiannis, L.; Mossou, E.; Forsyth, V. T.; Mitchell, E. P.; Mitraki, A.; Archontis, Georgios Z. (2014)
      The self-assembly of short peptides into fibrous nanostructures (such as fibrils and tubes) has recently become the subject of intense theoretical and experimental scrutiny, as such assemblies are promising candidates for ...
    • Article  

      Self-diffusivity, hydrogen bonding and density of different water models in carbon nanotubes 

      Alexiadis, A.; Kassinos, Stavros C. (2008)
      In this paper, the density, hydrogen bonding and self-diffusivity of water confined in carbon nanotubes are investigated. Molecular dynamics is used to simulate a large variety of nanotubes with various water models. Our ...
    • Article  

      Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 

      Archontis, Georgios Z.; Simonson, T.; Moras, D.; Karplus, M. (1998)
      Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of ...
    • Article  

      Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamics 

      Ioannou, F.; Archontis, Georgios Z.; Leontidis, Epameinondas (2011)
      We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space ...
    • Article  

      Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamicsAAA 

      Ioannou, F.; Archontis, Georgios Z.; Leontidis, Epameinondas (2011)
      We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space ...
    • Article  

      Transient isotopic kinetic study of the NO/H2/O2 (lean de-NOx) reaction on Pt/SiO2 and Pt/La-Ce-Mn-O catalysts 

      Costa, Costas N.; Efstathiou, Angelos M. (2004)
      Steady-state isotopic transient kinetic analysis (SSITKA) coupled with temperature-programmed surface reaction (TPSR) methods and using in situ mass spectroscopy and DRIFTS have been applied for the first time to study ...
    • Article  

      Wetting of doped carbon nanotubes by water droplets 

      Kotsalis, E. M.; Demosthenous, E.; Walther, J. H.; Kassinos, Stavros C.; Koumoutsakos, P. (2005)
      We study the wetting of doped single- and multi-walled carbon nanotubes by water droplets using molecular dynamics simulations. Chemisorbed hydrogen is considered as a model of surface impurities. We study systems with ...