Browsing by Subject "simulation"

Now showing items 1-20 of 25

    • Article  

      Algorithmic mechanisms for reliable crowdsourcing computation under collusion 

      Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Pareja, D. (2015)
      We consider a computing system where a master processor assigns a task for execution to worker processors that may collude. We model the workers' decision of whether to comply (compute the task) or not (return a bogus ...
    • Article  

      Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water 

      Tamamis, Phanourios; Skourtis, Spiros S.; Morikis, D.; Lambris, J. D.; Archontis, Georgios Z. (2007)
      The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist ...
    • Article  

      Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin 

      Ioannou, Androulla; Lambrou, Alexandra; Daskalakis, Vangelis; Pinakoulaki, Eftychia (2017)
      Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2 − cordination to the heme Fe in the O-binding nitrito (O1[sbnd]N[dbnd]O2) mode and to the heme 2-vinyl position. Nitrite is a powerful ...
    • Article  

      Crystallographic and computational studies on 4-phenyl-N-(β-D- glucopyranosyl)-1H-1,2, 3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with α-D-glucose, N-acetyl-β-D- glucopyranosylamine and N-benzoyl-N′-β-D-glucopyranosyl urea binding 

      Alexacou, Kyra Melinda; Hayes, Joseph M.; Tiraidis, Costas; Zographos, Spyros E.; Leonidas, Demetres D.; Chrysina, Evangelia D.; Archontis, Georgios Z.; Oikonomakos, Nikos G.; Paul, J. V.; Varghese, B.; Loganathan, D. (2008)
      4-Phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its ...
    • Article  

      An efficient methodology for simulating earthquake-induced 3D pounding of buildings 

      Polycarpou, Panayiotis C.; Papaloizou, Loizos; Komodromos, Petros I. (2014)
      The current paper presents an efficient methodology for numerically simulating in three dimensions adjacent buildings that may experience pounding during strong earthquakes. In particular, a new approach to the numerical ...
    • Article  

      Experimental and theoretical studies on physico-chemical parameters affecting the solubility of phosphogypsum 

      Papanicolaou, F.; Antoniou, Stella; Pashalidis, Ioannis (2009)
      Phosphogypsum is a waste by-product of the phosphate fertilizer industry, which is usually disposed in the environment because of its restricted use in industrial applications. Physico-chemical conditions existing in stack ...
    • Article  

      Free energy simulations: The meaning of the individual contributions from a component analysis 

      Boresch, S.; Archontis, Georgios Z.; Karplus, M. (1994)
      A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred ...
    • Article  

      Hindcast of oil-spill pollution during the Lebanon crisis in the Eastern Mediterranean, July-August 2006 

      Coppini, G.; De Dominicis, M.; Zodiatis, George; Lardner, R.; Pinardi, N.; Santoleri, R.; Colella, S.; Bignami, F.; Hayes, D. R.; Soloviev, D.; Georgiou, Georgios C.; Kallos, George B. (2011)
      MOON (Mediterranean Operational Oceanography Network http://www.moon-oceanforecasting.eu) provides near-real-time information on oil-spill detection (ocean color and SAR) and predictions [ocean forecasts (MFS and CYCOFOS) ...
    • Article  

      Image-based multiscale modeling predicts tissue-level and network-level fiber reorganization in stretched cell-compacted collagen gels 

      Barocas, V. Η; Sander, E. A.; Stylianopoulos, T.; Tranquillo, R. T. (2009)
      The mechanical environment plays an important role in cell signaling and tissue homeostasis. Unraveling connections between externally applied loads and the cellular response is often confounded by extracellular matrix ...
    • Article  

      K-string tensions in SU(N) gauge theories 

      Del Debbio, L.; Panagopoulos, Haralambos G.; Rossi, P.; Vicari, E. (2002)
      In the context of four-dimensional SU(N) gauge theories, we study the spectrum of the confining strings. We compute, for the SU(6) gauge theory formulated on a lattice, the three independent string tensions σk related to ...
    • Article  

      Lattice free energy with overlap fermions: A two-loop result 

      Athenodorou, A.; Panagopoulos, Haralambos G. (2004)
      We calculate the two-loop partition function of QCD on the lattice, using the Wilson formulation for gluons and the overlap-Dirac operator for fermions. Direct by-products of our result are the two-loop free energy and ...
    • Article  

      Measurement of the polar-angle distribution of leptons from W boson decay as a function of the W transverse momentum in pp̄ collisions at √s=1.8 TeV 

      Acosta, D.; Affolder, T.; Albrow, M. G.; Ambrose, D.; Amidei, D.; Anikeev, K.; Antos, J.; Apollinari, G.; Arisawa, T.; Artikov, A.; Ashmanskas, W.; Azfar, F.; Azzi-Bacchetta, P.; Bacchetta, N.; Bachacou, H.; Badgett, W.; 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.; Beretvas, Andrew; Bhatti, A.; Binkley, M.; Bisello, D.; Bishai, M.; Blair, R. E.; Blocker, C.; Bloom, K.; Blumenfeld, B.; Bocci, A.; Bodek, A.; Bolla, G.; Bolshov, A.; Bortoletto, D.; Boudreau, J.; Bromberg, C.; Brubaker, E.; Budagov, J.; Budd, H. S.; Burkett, K.; Busetto, G.; Byrum, K. L.; Cabrera, S.; Campbell, M.; Carithers, W.; Carlsmith, D.; Castro, A.; Cauz, D.; Cerri, A.; Cerrito, L.; Chapman, J.; Chen, C.; Chen, Y. C.; Chertok, M.; Chiarelli, G.; Chlachidze, G.; Chlebana, F.; Chu, M. L.; Chung, J. Y.; Chung, W. H.; Chung, Y. S.; Ciobanu, C. I.; Clark, A. G.; Coca, M.; Connolly, A.; Convery, M.; Conway, J.; Cordelli, M.; Cranshaw, J.; Culbertson, R.; Dagenhart, D.; D'Auria, S.; de Barbaro, P.; de Cecco, S.; Dell'Agnello, Simone; Dell'Orso, M.; Demers, S.; Demortier, L.; Deninno, M.; de Pedis, D.; Derwent, P. F.; Dionisi, Carlo; Dittmann, J. R.; Dominguez, A.; Donati, S.; D'Onofrio, M.; Dorigo, T.; Eddy, N.; Erbacher, R.; Errede, D.; Errede, S.; Eusebi, R.; 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.; Friedman, J.; Furic, I.; Gallinaro, M.; Garcia-Sciveres, M.; Garfinkel, A. F.; 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; Gresele, A.; Grosso-Pilcher, C.; Guenther, M.; Guimaraes da Costa, J.; Haber, C.; Hahn, S. R.; Halkiadakis, Eva; Handler, R.; Happacher, F.; Hara, K.; Harris, R. M.; Hartmann, F.; Hatakeyama, K.; Hauser, J.; Haywood, S. J.; Heinrich, J.; Hennecke, M.; Herndon, M.; Hill, C.; Hocker, A.; Hoffman, K. D.; Hou, S.; Huffman, B. T.; Hughes, R.; Huston, J.; Issever, C.; Incandela, J.; Introzzi, G.; Iori, M.; Ivanov, A.; Iwata, Y.; Iyutin, B.; James, E.; Jones, M.; Kamon, T.; Kang, J.; Karagoz Unel, M.; Kartal, S.; Kasha, H.; Kato, Y.; Kennedy, R. D.; Kephart, R.; Kilminster, B.; Kim, D. H.; Kim, H. S.; Kim, M. J.; Kim, S. B.; Kim, S. H.; Kim, T. H.; Kim, Y. K.; Kirby, M.; Kirsch, L.; Klimenko, S.; Koehn, P.; Kondo, K.; Konigsberg, J.; Korn, A.; Korytov, A.; Kroll, J.; Kruse, M.; Krutelyov, V.; Kuhlmann, S. E.; Kuznetsova, N.; Laasanen, A. T.; 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, T.; Litvintsev, D. O.; Lockyer, N. S.; Loginov, A.; Loreti, M.; Lucchesi, D.; Lukens, P.; Lyons, L.; Lys, J.; Madrak, R.; Maeshima, K.; Maksimovic, P.; Malferrari, L.; Mangano, M.; Manca, G.; Mariotti, M.; Martin, M.; Martin, A.; Martin, V.; Martínez, M.; Mazzanti, P.; McFarland, K. S.; McIntyre, P.; Menguzzato, M.; Menzione, A.; Merkel, P.; Mesropian, C.; Meyer, A.; Miao, T.; Miller, R.; Miller, J. S.; Miscetti, S.; Mitselmakher, G.; Moggi, N.; Moore, R.; Moulik, T.; Mulhearn, M.; Mukherjee, A.; Muller, T.; Munar, A.; Murat, P.; Nachtman, J.; Nahn, S.; Nakano, I.; Napora, R.; Niell, F.; Nelson, C.; Nelson, T.; Neu, C.; Neubauer, M. S.; Newman-Holmes, C.; Nigmanov, T.; Nodulman, L.; Oh, S. H.; Oh, Y. D.; Ohsugi, T.; Okusawa, T.; Orejudos, W.; Pagliarone, C.; Palmonari, F.; Paoletti, R.; Papadimitriou, Vaia; Patrick, J.; Pauletta, G.; Paulini, M.; Pauly, T.; Paus, C.; Pellett, D.; Penzo, A.; Phillips, T. J.; Piacentino, G.; Piedra, J.; Pitts, K. T.; Pompoš, A.; Pondrom, L.; Pope, G.; Pratt, T.; Prokoshin, F.; Proudfoot, J.; Ptohos, Fotios; Poukhov, O.; Punzi, G.; Rademacker, J.; Rakitine, A.; Ratnikov, F.; Ray, H.; Reichold, A.; Renton, P.; Rescigno, M.; Rimondi, F.; Ristori, L.; Robertson, W. J.; Rodrigo, T.; Rolli, S.; Rosenson, L.; Roser, R.; Rossin, R.; Rott, C.; Roy, A.; Ruiz, A.; Ryan, D.; Safonov, A.; Denis, R. S.; Sakumoto, W. K.; Saltzberg, D.; Sanchez, C.; Sansoni, A.; Santi, L.; Sarkar, S.; Savard, P.; Savoy-Navarro, A.; Schlabach, P.; Schmidt, E. E.; Schmidt, M. P.; Schmitt, M.; Scodellaro, L.; Scribano, A.; Sedov, A.; Seidel, S.; Seiya, Y.; Semenov, A.; Semeria, F.; Shapiro, M. D.; Shepard, P. F.; Shibayama, T.; Shimojima, M.; Shochet, M.; Sidoti, A.; Sill, A.; Sinervo, P.; Slaughter, A. J.; Sliwa, K.; Snider, F. D.; Snihur, R.; Spezziga, M.; Spinella, F.; Spiropulu, Maria; Spiegel, L.; Stefanini, A.; Strologas, John; Stuart, D.; Sukhanov, A.; Sumorok, K.; Suzuki, T.; Takashima, R.; Takikawa, K.; Tanaka, M.; Tecchio, M.; Tesarek, R. J.; Teng, P. K.; Terashi, K.; Tether, S.; Thom, J.; Thompson, A. S.; Thomson, E.; Tipton, P.; Tkaczyk, S.; Toback, D.; Tollefson, K.; Tonelli, D.; Tönnesmann, M.; Toyoda, H.; Trischuk, W.; Tseng, J.; Tsybychev, D.; Turini, N.; Ukegawa, F.; Unverhau, T.; Vaiciulis, T.; Varganov, A.; Vataga, E.; Vejcik III, S.; Velev, G.; Veramendi, G.; Vidal, R.; Vila, I.; Vilar, R.; Volobouev, I.; von der Mey, M.; Wagner, R. G.; Wagner, R. L.; Wagner, W.; Wan, Z.; Wang, C.; Wang, M. J.; Wang, S. M.; Ward, B.; Waschke, S.; Waters, D.; Watts, T.; Weber, M.; Wester III, W. C.; Whitehouse, B.; Wicklund, A. B.; Wicklund, E.; Williams, H. H.; Wilson, P.; Winer, B. L.; Wolbers, S.; Wolter, M.; Worm, S.; Wu, X.; Wurthwein, F.; Yang, U. K.; Yao, W.; Yeh, G. P.; Yi, K.; Yoh, J.; Yoshida, T.; Yu, I.; Yu, S.; Yun, J. C.; Zanello, L.; Zanetti, A.; Zetti, F.; Zucchelli, S. (2004)
      We present a measurement of the polar-angle distribution of leptons from W boson decay, as a function of the W transverse momentum. The measurement uses an 80±4 pb-1 sample of pp̄ collisions at √s = 1.8 TeV collected by ...
    • Article  

      Measuring input synchrony in the Ornstein-Uhlenbeck neuronal model through input parameter estimation 

      Koutsou, Achilleas; Kanev, J.; Christodoulou, Chris C. (2013)
      We present a method of estimating the input parameters and through them, the input synchrony, of a stochastic leaky integrate-and-fire neuronal model based on the Ornstein-Uhlenbeck process when it is driven by time-dependent ...
    • Article  

      Multiscale biphasic modelling of peritumoural collagen microstructure: The effect of tumour growth on permeability and fluid flow 

      Wijeratne, P. A.; Hipwell, J. H.; Hawkes, D. J.; Stylianopoulos, T.; Vavourakis, V. (2017)
      We present an in-silico model of avascular poroelastic tumour growth coupled with a multiscale biphasic description of the tumour–host environment. The model is specified to in-vitro data, facilitating biophysically realistic ...
    • Article  

      Multiscale modelling of solid tumour growth: the effect of collagen micromechanics 

      Wijeratne, P. A.; Vavourakis, V.; Hipwell, J. H.; Voutouri, C.; Papageorgis, P.; Stylianopoulos, T.; Evans, A.; Hawkes, D. J. (2016)
      Here we introduce a model of solid tumour growth coupled with a multiscale biomechanical description of the tumour microenvironment, which facilitates the explicit simulation of fibre–fibre and tumour–fibre interactions. ...
    • Article  

      On learning time delays between the spikes from different input neurons in a biophysical model of a pyramidal neuron 

      Koutsou, Achilleas; Bugmann, G.; Christodoulou, Chris C. (2015)
      Biological systems are able to recognise temporal sequences of stimuli or compute in the temporal domain. In this paper we are exploring whether a biophysical model of a pyramidal neuron can detect and learn systematic ...
    • Article  

      On the firing variability of the integrate-and-fire neurons with partial reset in the presence of inhibition 

      Christodoulou, Chris C. (2002)
      It has been reported (Phys. Rev. Lett. 82 (1999) 4731) that the firing variability of integrate-and-fire (I&F) neurons is strongly dependent on the level of inhibitory input unlike the Hodgkin-Huxley and FitzHugh-Nagumo ...
    • Article  

      Proton binding to proteins: A free-energy component analysis using a dielectric continuum model 

      Archontis, Georgios Z.; Simonson, T. (2005)
      Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...
    • Article  

      Robust estimation methods for a class of log-linear count time series models 

      Kitromilidou, S.; Fokianos, Konstantinos (2016)
      We study robust estimation of a log-linear Poisson model for count time series analysis. More specifically, we study robust versions of maximum likelihood estimators (MLEs) under three different forms of interventions: ...
    • Article  

      Self-assembly of phenylalanine oligopeptides: Insights from experiments and simulations 

      Tamamis, Phanourios; Adler-Abramovich, L.; Reches, M.; Marshall, K.; Sikorski, P.; Serpell, L.; Gazit, E.; Archontis, Georgios Z. (2009)
      Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into ...