Publications

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2011

  • Sameh, A., Arbenz, P. & Saad, Y. (2011). Guest editorial: Special issue on Parallel Matrix Algorithms and Applications (PMAA'10). Parallel Computing, 37(12), 731-732. [More] [Bibtex] [RIS]
  • Burkhart, H. & Christen, M (2011). \textscPatus: A Code Generation and Autotuning Framework For Parallel Iterative Stencil Computations on Modern Microarchitectures. In Proc. IEEE Int'l Parallel & Distributed Processing Symposium (IPDPS 2011), pages 1-12. [More] [Bibtex] [RIS]
  • Huber, J. & Grote, M (2011). Inexact interior-point methods for time-harmonic inverse medium problems. In Proc. of 10th International Conference on Mathematical and Numerical Aspects of Waves (Waves 2011), Vancouver, Canada. [More] [Bibtex] [RIS]
  • Burkhart, H. & Christen, M (2011). Automatic Code Generation and Tuning for Stencil Kernels on Modern Microarchitectures. In Proc. Int'l Supercomputing Conference (ISC 2011), pages 205-210. [More] [Bibtex] [RIS]
  • Burkhart, H., Christen, M., Rietmann, M. & Sathe, M (2011). Run, Stencil, Run! A Comparison of Modern Parallel Programming Paradigms. In PARS-Mitteilungen 2011. [More] [Bibtex] [RIS]
  • Bronstein, A. M., Zhang, C. & Kimmel, R. (2011). Are MSER features really interesting?. IEEE Trans. Pattern Analysis and Machine Intelligence (PAMI), 33(11), 2316-2320. [More] [Bibtex] [RIS]
  • Bronstein, A. M. & Litman, R. (2011). Diffusion-geometric maximally stable component detection in deformable shapes. Computers and Graphics, 35(3). [More] [Digital version] [Bibtex] [RIS]
  • Bronstein, A. M., Guibas, L. J. & Ovsjanikov, M. (2011). Shape Google: geometric words and expressions for invariant shape retrieval. ACM Trans. Graphics (TOG), 30(1), 1-20. [More] [Bibtex] [RIS]
  • Bronstein, A. M. (2011). Shape recognition with spectral distances. IEEE Trans. Pattern Analysis and Machine Intelligence (PAMI), 35(5), 1065-1071. [More] [Bibtex] [RIS]
  • Kovnatsky, A., Bronstein, A. M. & Kimmel, R (2011). Photometric heat kernel signatures. In Proc. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM). [More] [Bibtex] [RIS]
  • Hooda, A., Bronstein, A. M. & Horaud, R (2011). Shape palindromes: analysis of intrinsic symmetries in 2D articulated shapes. In Proc. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM). [More] [Bibtex] [RIS]
  • Bronstein, A. M., Aflalo, J. & Kimmel, R (2011). Deformable shape retrieval by learning diffusion kernels. In Proc. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM). [More] [Bibtex] [RIS]
  • Bronstein, A. M., Wolf, A., Rosman, G. & Kimmel, R (2011). Group-valued regularization framework for motion segmentation of dynamic non-rigid shapes. In Proc. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM). [More] [Bibtex] [RIS]
  • Bronstein, A. M., Wang, C. & Paragios, N (2011). Discrete minimum distortion correspondence problems for non-rigid shape matching. In Proc. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM). [More] [Bibtex] [RIS]
  • Kovnatsky, A., Bronstein, A. M., Zaharescu, A., Bustos, B., Smeets, D., Vandermeulen, D. et al (2011). SHREC 2011: robust feature detection and description benchmark. In Proc. EUROGRAPHICS Workshop on 3D Object Retrieval (3DOR). [More] [Bibtex] [RIS]
  • Bronstein, A. M., Michel, F. & Paragios, N (2011). Boosted metric learning for 3D multi-modal deformable registration. In Proc. Intl. Symposium on Biomedical Imaging (ISBI). [More] [Bibtex] [RIS]
  • Kovnatsky, A., Bronstein, A. M., Zaharescu, A., Bustos, B., Smeets, D., Vandermeulen, D. et al. (2011). SHREC 2011: robust feature detection and description benchmark. [More] [Bibtex] [RIS]
  • Kovnatsky, A., Bronstein, A. M. & Kimmel, R. (2011). Diffusion framework for geometric and photometric data fusion in non-rigid shape analysis. [More] [Bibtex] [RIS]

2010

  • Steiner, J (2010). Cosserat-Rods and Elastic Bodies: On the Numerical Simulation of a Coupled System. In Middleton, J. & Jacobs, C. (editors), CMBBE2010 : 9th International Symposium on Computer methods in Biomechanics and Biomedical Engineering, Valencia, Spain. Valencia, Spain : Arup, Solihull. [More] [Bibtex] [RIS]
  • Groß, C. (2010). The Linear Algebra Module in ObsLib++ - Description, Comparisons and Numerical Results, Institute for Numerical Simulation, Bonn and Institute of Computational Science, Università della Svizzera Italiana. [More] [Bibtex] [RIS]
  • Groß, C., Steiner, J., Krause & Rolf. (2010). Heterogeneous Coupling: A Comparison of two Approaches for the Modeling of thin Structures. PAMM, 10(1), 649-650. [More] [Digital version] [Bibtex] [RIS]
  • Groß, C (2010). Nonlinear Decomposition Methods in Elastodynamics. In Kreiss, G., Lötstedt, P., Målqvist, A. & Neytcheva, M. (editors), Numerical Mathematics and Advanced Applications 2009, pages 407-415. Springer. [More] [Bibtex] [RIS]
  • Noé, F., Prinz, J. -. & Held, M. (2010). Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100(3), 701-710. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. & Weber, M. (2010). Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82(3), 031114. [More] [Digital version] [Bibtex] [RIS]
  • Horenko & Illia. (2010). Finite element approach to clustering of multidimensional time series. J. of Sci. Comp., 32(1), 62-83. [More] [Digital version] [Bibtex] [RIS]
  • Horenko & Illia. (2010). On identification of non-stationary factor models and its application to atmospherical data analysis. J. Atmos. Sci., 67(5), 1559-1574. [More] [Bibtex] [RIS]
  • Horenko & Illia. (2010). On clustering of non-stationary meteorological time series. Dyn. of Atm. and Oc., 49(2-3), 164-187. [More] [Digital version] [Bibtex] [RIS]
  • Becherer, D. (2010). Optimial Allocation of a Futures Portfolio Utilizing Numerical Market Phase Detection. J. Finan. Math., 1(1), 752-779. [More] [Bibtex] [RIS]
  • Schütte, C. (2010). On metastable conformational analysis of non-equilibrium biomolecular time series. Mult. Mod. Sym., 8(2), 701-716. [More] [Digital version] [Bibtex] [RIS]
  • Bronstein, A. M., Raviv, D., Sochen, N. & Kimmel, R. (2010). Affine-invariant geodesic geometry of deformable 3D shapes. [More] [Bibtex] [RIS]
  • Bronstein, A. M., Raviv, D., Sochen, N. & Kimmel, R. (2010). Affine-invariant diffusion geometry for the analysis of deformable 3D shapes. [More] [Bibtex] [RIS]
  • Groß, C. (2010). A Generalized Recursive Trust-Region Approach - Nonlinear Multiplicatively Preconditioned Trust-Region Methods and Applications, Institute of Computational Science, Universita della Svizzera italiana. [More] [Bibtex] [RIS]
  • Fackeldey, K (2010). Numerical Validation of Constraints Based Multiscale Methods. In Griebel, M. & Schweitzer, M. A. (editors), Proc. Meshfree Methods for Partial Differential Equations V, pages 141 - 154. [More] [Bibtex] [RIS]
  • Vinet, A., Linnenbank, A. C., Reimer, A. G., Verkerk, A. O., Wilde, A. A., Bezzina, C. R. et al. (2010). Mechanism of Right Precordial ST-Segment Elevation in Structural Heart Disease: Excitation Failure by Current-to-Load Mismatch. Heart Rhythm, 7, 238-248. [More] [Bibtex] [RIS]
  • Vinet, A. & Comtois, P. (2010). Approche multi-échelle à la modélisation de l'activité électrique du coeur. Médecine/sciences, 26(1), 57-63. [More] [Bibtex] [RIS]
  • Neufeld, E., Burkhart, H., Christen, M. & Paulides, M (2010). Manycore Stencil Computations in Hyperthermia Applications. In Dongarra, J., Bader, D. & Kurzak, J. (editors), Scientific Computing with Multicore and Accelerators. CRC Press. [More] [Bibtex] [RIS]
  • Wächter, A. & Curtis, F. (2010). An Interior-Point Algorithm for Large-Scale Nonlinear Optimization with Inexact Step Computations. SIAM J. Scientific Computing, 32(6), 3447-3475. [More] [Bibtex] [RIS]
  • Bronstein, A. M. & Litman, R. (2010). Diffusion-geometric maximally stable component detection in deformable shapes. [More] [Bibtex] [RIS]

2009

  • Krause, Rolf, Walloth & Mirjam. (2009). A Time Discretization Scheme Based on Rothe's Method for Dynamical Contact Problems with Friction. Computer Methods in Applied Mechanics and Engineering, 199(1-4), 1-19. [More] [Bibtex] [RIS]
  • Neufeld, E., Burkhart, H., Christen, M. & Messmer, P (2009). Parallel Data-Locality Aware Stencil Computations on Modern Micro-Architectures. In Proc. IEEE Int'l Parallel & Distributed Processing Symposium (IPDPS 2009), pages 1-10. [More] [Bibtex] [RIS]
  • Mohr, C. (2009). Level set based multi-scale methods for large deformation contact problems. Applied Numerical Mathematics, 61(4), 428-442. [More] [Bibtex] [RIS]
  • Krause & Rolf. (2009). A Non-Smooth Multiscale Method for Solving Frictional Two-Body Contact Problems in 2D and 3D with Multigrid Efficiency. SIAM Journal on Scientific Computing, 31(2), 1399-1423. [More] [Bibtex] [RIS]
  • Dickopf, Thomas, Krause & Rolf (2009). Weak information transfer between non-matching warped interfaces. In ~Bercovier, M., ~Gander, M., ~Kornhuber, R. & ~Widlund, O. (editors), Domain Decomposition Methods in Science and Engineering XVIII. Berlin : Springer. [More] [Digital version] [Bibtex] [RIS]
  • Klipp, E., Hasenbrink, G., Lichtenberg-Frat$acute{e}$, H., Ludwig, J., van Heusden, P. & Hendriksen, W. (2009). Graphical analysis and experimental evaluation of \textitSaccharomyces cerevisiae $P_{TRK_{1|2}}$ and $P_{BMH_{1|2}}$ promoter region. Genome Informatics, 21, 11-20. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. & Vanden-Eijnden, E. (2009). Transition Path Theory for Markov Jump-Processes. Mult. Mod. Sim., 7(3), 1192-1219. [More] [Digital version] [Bibtex] [RIS]
  • Hartmann, C., Schütte, C., Meerbach, E. & Noé, F (2009). Conformation Dynamics. In Jeltsch, I. & Wanner, G. (editors), Proceedings of the 6th International Congress on Industrial and Applied Mathematics, pages 297-335. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. & Noé, F. (2009). Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80(2), 021106. [More] [Digital version] [Bibtex] [RIS]
  • Majda, A., Franzke, C. & Klein, R. (2009). Systematic Metastable Atmospheric Regime Identification in an AGCM. J. Atmos. Sci., 66(7), 2579-2599. [More] [Digital version] [Bibtex] [RIS]
  • Horenko & Illia. (2009). On robust estimation of low-frequency variability trends in discrete Markovian sequences of Atmospherical Circulation Patterns. J. Atmos. Sci., 66(7), 2059-2072. [More] [Digital version] [Bibtex] [RIS]
  • Dickopf, Thomas, Krause & Rolf. (2009). A contact method for parametric finite elements, Institute of Computational Science. [More] [Bibtex] [RIS]
  • Groß, C. (2009). A new Class of Non--linear Additively Preconditioned Trust--Region Strategies: Convergence Results and Applications to Non-linear Mechanics, Institute for Numerical Simulation, University of Bonn. [More] [Bibtex] [RIS]
  • Groß, C. (2009). On the Convergence of Recursive Trust--Region Methods for Multiscale Non-linear Optimization and Applications to Non-linear Mechanics. SIAM J. Numer. Anal., 47(4), 3044-3069. [More] [Bibtex] [RIS]
  • Groß, C (2009). A Recursive Trust--Region Method for Non-convex Constrained Minimization. In Domain Decomposition Methods in Science and Engineering XVIII, pages 137-144. [More] [Bibtex] [RIS]
  • Fackeldey, K. (2009). Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics. Int. J. Numer. Meth. Engng, 79(12), 1517-1535. [More] [Bibtex] [RIS]
  • Dickopf, T. (2009). Efficient simulation of multi-body contact problems on complex geometries: A flexible decomposition approach using constrained minimization. International Journal for Numerical Methods in Engineering, 77(13), 1834-1862. [More] [Bibtex] [RIS]
  • Dickopf, T (2009). Weak information transfer between non-matching warped interfaces. Domain Decomposition Methods in Science and Engineering XVIII. [More] [Bibtex] [RIS]
  • Dickopf, T. (2009). A pseudo-{$L^2$}-projection for multilevel methods based on non-nested meshes., Institute of Computational Science. [More] [Bibtex] [RIS]
  • Dickopf, T. (2009). A study of prolongation operators between non-nested meshes, Institute of Computational Science. [More] [Bibtex] [RIS]
  • Fackeldey, D. K (2009). Weak Coupling Algorithms in Multiscale Simulations. In Proceedings of the third Inter. Confer. on Comp. Meth. for Coupled Problems in Science and Engrg.. [More] [Bibtex] [RIS]
  • Vinet, A. & Dubé, B. (2009). Cardiac Anisotropy in Boundary-Element Models for the Electrocardiogram. mbec, 47, 719-729. [More] [Bibtex] [RIS]
  • Essebag, V. (2009). Guidance for catheter ablation of ventricular arrhythmia. mbec, 47, 241-243. [More] [Bibtex] [RIS]
  • Vinet, A., Coronel, R. & Opthof, T. (2009). Validation of a simple model for the morphology of the T wave in unipolar electrograms. ajph, 297, H792-801. [More] [Bibtex] [RIS]
  • Wächter, A. & Weiser, M. (2009). Algebraic Multilevel Preconditioner For the Helmholtz Equation In Heterogeneous Media. SIAM J. Scientific Computing, 31(2), 3781-3805. [More] [Bibtex] [RIS]
  • Sameh, A., Christen, M., Manguoglu, M. & Sathe, M. (2009). Parallel Scalable PDE-Constrained Optimization: Antenna Identification in Hyperthermia Cancer Treatment Planning. Journal Computer Science Research and Development, Proceedings of the International Supercomputing Conference ISC09., 3--4, 177-183. [More] [Bibtex] [RIS]
  • Sameh, A. & Manguoglu, M. (2009). PSPIKE Parallel Sparse Linear System Solver. Proceedings of the 15th International Euro-Par Conference on Parallel Processing, Lecture Notes in Computer Science, , 797-808. [More] [Bibtex] [RIS]
  • Bronstein, A. M. & Kimmel, R. (2009). Numerical geometry of non-rigid shapes. New York : Springer. [More] [Bibtex] [RIS]

2008

  • Groß, C. (2008). Import of Geometries and Extended Informations into Obslib++ using the Exodus II and Exodus Parameter File Formats, Institute for Numerical Simulation. [More] [Bibtex] [RIS]
  • Raccanelli, A. (2008). Vorrichtung zur Erzeugung eines homogenen Magnetfelds und Optimierungsverfahren, University of Bonn and FZT Juelich. [More] [Bibtex] [RIS]
  • Bakker, B., Klipp, E. & Assmus, H. (2008). Drug-efficacy depends on the inhibitor type and the target position in a metabolic network - a systematic study. J. Theor. Biol., 252(3), 442-455. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. (2008). Likelihood-based estimation of multidimensional Langevin models and its application to biomolecular dynamics. Mult. Mod. Sim., 7(2), 802-827. [More] [Digital version] [Bibtex] [RIS]
  • Horenko & Illia. (2008). On simultaneous data-based dimension reduction and hidden phase identification. J. Atmos. Sci., 65(6), 1941-1954. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C., Klein, R. & Dolaptchiev, S. (2008). Automated generation of reduced stochastic weather models I: Simultaneous dimension and model reduction for time series analysis. Mult. Mod. Sim., 6(4), 1125-1145. [More] [Digital version] [Bibtex] [RIS]
  • Eliseev, A., Mokhov, I., Klein, R. & Dolaptchiev, S. (2008). Metastable decomposition of high-dimensional meteorological data with gaps. J. Atmos. Sci., 65(10), 1-19. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C., Dittmer, E., Lankas, F. & Maddocks, J. (2008). Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Applications to B-DNA. J. Appl. Dyn. Syst., 7(2), 563-560. [More] [Digital version] [Bibtex] [RIS]
  • Groß, C., Mohr, C., Steiner, J., Krause, R. & Dickopf, T (2008). Efficient Simulation Techniques for Heterogeneous Models in Biomechanics. In Proceedings of the 8th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering. [More] [Bibtex] [RIS]
  • Fackeldey, K (2008). Quadrature and Implementation of the Weak Coupling Method. In Proceedings of the fourth Int. Conf. Multiscale Materials Modeling, pages 62-65. [More] [Bibtex] [RIS]
  • Fackeldey, K. (2008). CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach. PAMM, 8(1), 10495. [More] [Bibtex] [RIS]
  • Fackeldey, K. & Schweitzer, M. A (2008). Stability of Energy Transfer in the Weak Coupling Method. In Meshfree Methods for Partial Differential Equations IV, pages 111-119. [More] [Bibtex] [RIS]
  • {D}euflhard, P., {K}rause, R. & {E}rtel, S. (2008). A Contact--Stabilized Newmark Method for Dynamical Contact Problems. International Journal for Numerical Methods in Engineering, 73(9), 1274 - 1290. [More] [Bibtex] [RIS]
  • {S}ander, O., Deuflhard, P., Kornhuber, R. & Ertel, S. (2008). A Monotone Multigrid Solver for Two Body Contact Problems in Biomechanics. Computing and Visualization in Science, 11(1), 3-15. [More] [Bibtex] [RIS]
  • Groß, C. & Berrenberg, S (2008). Numerical Simulation in Biomechanics: A Flexible Approach.. In 8th World Congress on Computational Mechanics and 5th European Congress on Computational Methods in Applied Sciences and Engineering. [More] [Bibtex] [RIS]
  • Wächter, A. & Weiser, M. (2008). Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization. SIAM J. Scientific Computing, 31(2), 939-960. [More] [Bibtex] [RIS]
  • Bollhöfer, M. & Römer, R. A. (2008). On Large Scale Diagonalization Techniques For The Anderson Model Of Localization. SIAM Review, 50(1), 91-112. [More] [Bibtex] [RIS]
  • Burkhart, H. & Christen, M. (2008). Algorithmic Performance Studies on Graphics Processing Unit. J. Parallel and Distrib. Comput., 28, 1360-1369. [More] [Bibtex] [RIS]
  • Neufeld, E., Burkhart, H., Christen, M. & Messmer, P (2008). Accelerating Stencil-Based Computations by Increased Temporal Locality on Modern Multi- and Many-Core Architectures. In Proc. of First International Workshop on New Frontiers in High-performance and Hardware-aware Computing (HipHaC'08), pages 47-54. Universitätsverlag Karlsruhe. [More] [Bibtex] [RIS]

2007

  • Berrenberg, S. (2007). Efficient Parallel Simulation of Biphasic Materials in Biomechanics. Sixth International Congress on Industrial Applied Mathematics (ICIAM07) and GAMM Annual Meeting, Z\"urich 2007, 7(1), 1121101-1121102. [More] [Bibtex] [RIS]
  • Burkhart, H. & Christen, M (2007). General-Purpose Sparse Matrix Building Blocks using the NVIDIA CUDA Technology Platforma. In Proc. of First Workshop on General Purpose Processing on Graphics Processing Units, Northeastern University, Boston. [More] [Bibtex] [RIS]
  • Wächter, A. & Hagemann, M. (2007). Matching-based Preprocessing Algorithms to the Solution of Saddle-Point Problems in Large-Scale Nonconvex Interior-Point Optimization. Comput. Optim. Appl., 36(2-3), 321-341. [More] [Bibtex] [RIS]
  • Krause & Rolf (2007). On the Multiscale Solution of Constrained Minimization Problems. In Proceedings of the 17th International. Conference on Domain Decomposition Methods. [More] [Bibtex] [RIS]
  • Gerber & Susanne. (2007). Perfusionsmodellierung in menschlichen Tumoren. Master Thesis, Freie Universitr\"{Š}t Berlin, Konrad-Zuse-Zentrum fŸr Informationstechnik Berlin (ZIB). [More] [Digital version] [Bibtex] [RIS]
  • Putzig & Lars. (2007). Soft contraints - A penalty approach to the superhedging problem. Master Thesis. [More] [Bibtex] [RIS]
  • Metzner & Philipp. (2007). Transition Path Theory for Markov Processes. Phd Thesis, Free University of Berlin. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C., Dittmer, E. & Jahnke, T. (2007). Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227(1), 353-375. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. (2007). Generator estimation of Markov jump processes based on incomplete observations nonequidistant in time. Physical Review E, 227(1), 353-375. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C. (2007). Generator estimation of Markov Jump processes based on incomplete observations nonequidistant in time. Physical Review E, 227(1), 353-375. [More] [Bibtex] [RIS]
  • Fischer, A., Schütte, C., Meerbach, E. & Waldhausen, S. (2007). Identification of biomolecular conformations from incomplete torsion angle observations by hidden Markov models. Journal of Computational Chemistry, 28(15), 2453-2464. [More] [Digital version] [Bibtex] [RIS]
  • Hartmann, C., Schütte, C. & Noé, F. (2007). Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76(1), 016706. [More] [Digital version] [Bibtex] [RIS]
  • Schütte, C., Noé, F. & Smith, J. C. (2007). Hierarchical Analysis of Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Chem. Phys., 126(15), 155102. [More] [Digital version] [Bibtex] [RIS]
  • Schmidt, B., Schütte, C. & Meerbach, E (2007). Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution. In K\"uhn, O. & Wöste, L. (editors), Analysis and Control of Ultrafast Photoinduces Reactions, pages 796-806. Springer. [More] [Digital version] [Bibtex] [RIS]
  • Raccanelli, A. & Dutz, H (2007). A Finite Element Model for the Thermal Transport in Solid Targets. In Proceedings of The 17th International Spin Physics Symposium (SPIN2006). [More] [Bibtex] [RIS]
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