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Boulanger J.,Radon Institute for Computational and Applied Mathematics | Boulanger J.,University Pierre and Marie Curie | Gidon A.,University Pierre and Marie Curie | Kervran C.,Institute National Of Recherche En Informatique Et En Automatique | And 2 more authors.
PLoS ONE | Year: 2010

Automatic detection and characterization of molecular behavior in large data sets obtained by fast imaging in advanced light microscopy become key issues to decipher the dynamic architectures and their coordination in the living cell. Automatic quantification of the number of sudden and transient events observed in fluorescence microscopy is discussed in this paper. We propose a calibrated method based on the comparison of image patches expected to distinguish sudden appearing/vanishing fluorescent spots from other motion behaviors such as lateral movements. We analyze the performances of two statistical control procedures and compare the proposed approach to a frame difference approach using the same controls on a benchmark of synthetic image sequences. We have then selected a molecular model related to membrane trafficking and considered real image sequences obtained in cells stably expressing an endocytic-recycling transmembrane protein, the Langerin-YFP, for validation. With this model, we targeted the efficient detection of fast and transient local fluorescence concentration arising in image sequences from a data base provided by two different microscopy modalities, wide field (WF) video microscopy using maximum intensity projection along the axial direction and total internal reflection fluorescence microscopy. Finally, the proposed detection method is briefly used to statistically explore the effect of several perturbations on the rate of transient events detected on the pilot biological model. © 2010 Boulanger et al. Source


Kugler P.,University of Hohenheim | Kugler P.,Radon Institute for Computational and Applied Mathematics
PLoS ONE | Year: 2016

Early after depolarizations (EADs) are pathological oscillations in cardiac action potentials during the repolarization phase and may be caused by drug side effects, ion channel disease or oxidative stress. The most widely observed EAD pattern is characterized by oscillations with growing amplitudes. So far, its occurence has been explained in terms of a supercritical Hopf bifurcation in the fast subsystem of the action potential dynamics from which stable limit cycles with growing amplitudes emerge. The novel contribution of this article is the introduction of two alternative explanations of EAD genesis with growing amplitudes that do not involve stable limit cycles in fast subsystems. In particular, we demonstrate that EAD patterns with growing amplitudes may alternatively arise due to a delayed subcritical Hopf bifurcation or an unstable manifold of a saddle focus fixed point in the full fast-slow system modelling the action potential. Our work extends the list of possible dynamical EAD mechanisms and may contribute to a classification of drug effects in preclinical cardiotoxicity testing. © 2016 Philipp Kügler. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source


Chamakuri N.,Radon Institute for Computational and Applied Mathematics | Engwer C.,University of Munster | Kunisch K.,Radon Institute for Computational and Applied Mathematics | Kunisch K.,University of Graz
Journal of Computational Physics | Year: 2014

Optimal control for cardiac electrophysiology based on the bidomain equations in conjunction with the Fenton-Karma ionic model is considered. This generic ventricular model approximates well the restitution properties and spiral wave behavior of more complex ionic models of cardiac action potentials. However, it is challenging due to the appearance of state-dependent discontinuities in the source terms. A computational framework for the numerical realization of optimal control problems is presented. Essential ingredients are a shape calculus based treatment of the sensitivities of the discontinuous source terms and a marching cubes algorithm to track iso-surface of excitation wavefronts. Numerical results exhibit successful defibrillation by applying an optimally controlled extracellular stimulus. © 2014 Elsevier Inc. Source


Lorenz N.,Radon Institute for Computational and Applied Mathematics | Offner G.,AVL List GmbH | Knaus O.,AVL List GmbH
Proceedings of the Institution of Mechanical Engineers, Part J: Journal of Engineering Tribology | Year: 2015

Journal bearings are key components in internal combustion engines. Their reliability, durability, and economy are of highest importance. Especially, the accurate prediction of friction loss power and wear are essential for the development of an engine. For an appropriate representation of the hydrodynamic load-carrying capacity and also the friction behavior, both the dynamics of the contacting components, the shape of the contacting component surfaces, the amount of the available lubricant, and the properties of the lubricant itself are of importance. A Reynolds-averaged equation with laminar flow conditions in combination with an asperity contact model is a typical modeling approach for that purpose. The lubricant properties are in particular influenced by its thermal conditions on one hand. On the other hand, the thermal conditions are influenced by the mixed lubricated contact conditions as well. These interactions require a coupled modeling approach, which combines the component flexibility and its interaction with load-carrying capacity as well as the thermal behavior of the lubricant and the component surfaces. In this work, a thermo-elasto-hydrodynamic contact model is presented, which computes the oil film temperature using a 2D energy equation. The 2D equation is derived from the equivalent 3D energy equation by integration over the clearance gap height. Besides component material properties such as specific heat capacity, density, heat conductivity for lubricant and structures, also heat transfer through mixed lubricated regimes and partly filled clearance gaps, as implied in cavitation regions, are being considered. The presented method is applied for a typical engineering task of a sensitivity analysis for oils with different viscosity index (VI) improvers in a main bearing of a four-cylinder inline diesel engine. The influence of the oil film temperature on the oil film viscosity and therefore on the load-carrying capacity is shown. Furthermore, the simplified 2D approach is compared with a 3D approach both in terms of obtained result data and in terms of elapsed calculation times. The presented results show similar accuracy of the 2D approach with significantly reduced simulation time compared to the equivalent 3D case. © IMechE 2014. Source


Gotschel S.,Zuse Institute Berlin | Chamakuri N.,Radon Institute for Computational and Applied Mathematics | Kunisch K.,Radon Institute for Computational and Applied Mathematics | Kunisch K.,University of Graz | Weiser M.,Zuse Institute Berlin
Journal of Scientific Computing | Year: 2014

This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples. © 2013 Springer Science+Business Media New York. Source

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