Browsing by Subject "computer simulation"

Now showing items 1-20 of 28

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      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 ...
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      Behavioral plasticity through the modulation of switch neurons 

      Vassiliades, Vassilis; Christodoulou, Chris C. (2016)
      A central question in artificial intelligence is how to design agents capable of switching between different behaviors in response to environmental changes. Taking inspiration from neuroscience, we address this problem by ...
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      CHARMM: The biomolecular simulation program 

      Brooks, B. R.; Brooks III, C. L.; Mackerell Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, Georgios Z.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009)
      CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...
    • Article  

      Computational protein design: The proteus software and selected applications 

      Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (2013)
      We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...
    • Article  

      Dispersed-phase structure in sheared MHD turbulence 

      Xu, X.; Rouson, D. W. I.; Kassinos, Stavros C.; Radhakrishnan, H. (2012)
      Direct numerical simulations are performed to examine particle dispersion in homogeneous turbulence subjected to mean shear and an externally applied magnetic field. We employ the Brucker et al. algorithm for simulating ...
    • Article  

      Distinguishing the causes of firing with themembrane potential slope 

      Koutsou, Achilleas; Christodoulou, Chris C.; Bugmann, G.; Kanev, J. (2012)
      In this letter, we aim to measure the relative contribution of coincidence detection and temporal integration to the firing of spikes of a simple neuron model. To this end, we develop a method to infer the degree of synchrony ...
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      Editorial 

      Lucas, P.; Rospars, J. -P; Christodoulou, Chris C. (2015)
    • Article  

      Editorial on the Special Issue “SimInhale” 

      Fattal, E.; Kassinos, Stavros C. (2018)
    • Article  

      The Effect of Head Rotation on the Geometry and Hemodynamics of Healthy Vertebral Arteries 

      Aristokleous, Nicolas; Seimenis, Ioannis; Georgiou, Georgios C.; Nicolaïdes, Andrew N.; Anayiotos, Andreas S. (2015)
      The geometric and hemodynamic characteristics of the left and right vertebral arteries (LVA, RVA) of six healthy volunteers were investigated for the supine (S) and the prone position (P) a common sleeping posture with ...
    • Article  

      An efficient computational fluid-particle dynamics method to predict deposition in a simplified approximation of the deep lung 

      Koullapis, P. G.; Hofemeier, P.; Sznitman, J.; Kassinos, Stavros C. (2018)
      High-fidelity simulations of the complete airway tree are still largely beyond current computational capabilities. Towards large-scale simulations of the human lung, the current study introduces a numerical methodology to ...
    • Article  

      Experimental measurements and mathematical modeling towards quantification of brain swelling stress 

      Angeli, S.; Stylianopoulos, T. (2017)
      Traumatic brain injury results in brain tissue swelling which can be a life threatening condition due to skull confinement. While previous efforts successfully measured the exhibited volume change in brain tissue swelling, ...
    • Article  

      Fluctuations in biological and bioinspired electron-transfer reactions 

      Skourtis, Spiros S.; Waldeck, D. H.; Beratan, David N. (2010)
      Central to theories of electron transfer (ET) is the idea that nuclear motion generates a transition state that enables electron flow to proceed, but nuclear motion also induces fluctuations in the donor-acceptor (DA) ...
    • Article  

      Free energy simulations come of age: Protein-ligand recognition 

      Simonson, T.; Archontis, Georgios Z.; Karplus, M. (2002)
      In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
    • Article  

      Impact of head rotation on the individualized common carotid flow and carotid bifurcation hemodynamics 

      Aristokleous, Nicolas; Seimenis, Ioannis; Georgiou, Georgios C.; Papaharilaou, Yannis; Brott, B. C.; Nicolaïdes, Andrew N.; Anayiotos, Andreas S. (2014)
      This paper aims at evaluating the changes that head rotation poses on morphological and flow characteristics of the carotid bifurcation (CB) and on the distribution of parameters that are regarded as important in atherosclerosis ...
    • Article  

      In silico assessment of mouth-throat effects on regional deposition in the upper tracheobronchial airways 

      Koullapis, P. G.; Nicolaou, L.; Kassinos, Stavros C. (2018)
      Regional deposition of inhaled medicines is a valuable metric of effectiveness in drug delivery applications to the lung. In silico methods are now emerging as a valuable tool for the detailed description of localized ...
    • Article  

      Large Eddy Simulation of near-bed pipelines in oscillatory flow 

      Fonias, E. N.; Grigoriadis, D. G. E. (2018)
      A series of unsteady, three-dimensional numerical simulations of the incompressible, oscillatory flow around a near-bed pipeline is presented. A flow at Reynolds number equal to Reαo=20,000 with respect to the oscillatory ...
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      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  

      Near Poisson-type firing produced by concurrent excitation and inhibition 

      Christodoulou, Chris C.; Bugmann, G. (2000)
      The effect of inhibition on the firing variability is examined in this paper using the biologically-inspired temporal noisy-leaky integrator (TNLI) neuron model. The TNLI incorporates hyperpolarising inhibition with negative ...
    • Article  

      New antimony(III) bromide complexes with thioamides: Synthesis, characterization, and cytostatic properties 

      Ozturk, I. I.; Hadjikakou, Sotiris K.; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Kubicki, Maciej; Tasiopoulos, Anastasios J.; Scleiman, H.; Barsan, M. M.; Butler, I. S.; Balzarini, J. (2009)
      New antimony(III) bromide complexes with the heterocyclic thioamides, thiourea (TU), 2-mercapto-1-methylimidazole (MMl), 2-mercapto-benzimidazole (MBZlM), 2-mercapto-5-methyl-benzimidazole (MMBZIM), 5-ethoxy-2-mercapto- ...