2023
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Sourav Ray, Konstantin Fackeldey, Christoph Stein, Marcus Weber |
Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane
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Biophysica, 3(2), pp. 263-275, 2023 |
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Christopher Secker, Konstantin Fackeldey, Marcus Weber, Sourav Ray, Christoph Gorgulla, Christof Schütte |
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists
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Journal of Cheminformatics, Vol.15, 2023 |
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Luca Donati, Konstantin Fackeldey, Marcus Weber |
PLANTS+: Improving Ant Colony Algorithms for Drug Design
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2023 (under review) |
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2022
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Konstantin Fackeldey, Mathias Oster, Leon Sallandt, Reinhold Schneider |
Approximative Policy Iteration for Exit Time Feedback Control Problems driven by Stochastic Differential Equations using Tensor Train format
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SIAM Journal on Multiscale Modeling and Simulation, 20(1), pp. 379-403, 2022 |
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arXiv
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Christoph Gorgulla, Abhilash Jayaraj, Konstantin Fackeldey, Haribabu Arthanari |
Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches
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Current Opinion in Chemical Biology, Vol.69, pp. 102156-102156-12, 2022 |
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N. Alexia Raharinirina, Konstantin Fackeldey, Marcus Weber |
Qualitative Euclidean embedding of Disjoint Sets of Points
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2022 |
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Renata Sechi, Konstantin Fackeldey, Surahit Chewle, Marcus Weber |
SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data
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Algorithms, 15(9), p. 297, 2022 |
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2021
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Christoph Gorgulla, Krishna M. Padmanabha Das, Kendra E Leigh, Marco Cespugli, Patrick D. Fischer, Zi-Fu Wang, Guilhem Tesseyre, Shreya Pandita, Alex Shnapir, Anthony Calderaio, Colin Hutcheson, Minko Gechev, Alexander Rose, Noam Lewis, Erez Yaffe, Roni Luxenburg, Henry D. Herce, Vedat Durmaz, Thanos D. Halazonetis, Konstantin Fackeldey, Justin J. Patten, Alexander Chuprina, Igor Dziuba, Alla Plekhova, Yurii Moroz, Dmytro Radchenko, Olga Tarkhanova, Irina Yavnyuk, Christian C. Gruber, Ryan Yust, Dave Payne, Anders M. Näär, Mark N. Namchuk, Robert A. Davey, Gerhard Wagner, Jamie Kinney, Haribabu Arthanari |
A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening
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iScience, 24(2), p. 102021, 2021 |
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Konstantin Fackeldey, Jonas Röhm, Amir Niknejad, Surahit Chewle, Marcus Weber |
Analyzing Raman Spectral Data without Separabiliy Assumption
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Journal of Mathematical Chemistry, 3(59), pp. 575-596, 2021 |
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arXiv
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Susanne Röhl, Marcus Weber, Konstantin Fackeldey |
Computing the minimal rebinding effect for non-reversible processes
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Multiscale Modeling and Simulation, 19(1), pp. 460-477, 2021 |
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arXiv
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N. Alexia Raharinirina, Marcus Weber, Ralph Birk, Konstantin Fackeldey, Sarah M. Klasse, Tonio Sebastian Richter |
Different Tools and Results for Correspondence Analysis
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2021 |
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Ralph Birk, N. Alexia Raharinirina, Konstantin Fackeldey, Tonio Sebastian Richter, Marcus Weber |
Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts
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2021 (in progress) |
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Isabel Nitzke, Konstantin Fackeldey, Jadran Vrabec |
Long range corrections for inhomogeneous fluids containing a droplet or a bubble
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Molecular Simulation, pp. 1-14, 2021 |
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Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber |
Neue Medikamente dank Supercomputern
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Spektrum der Wissenschaft, pp. 40-46, 2021 |
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Christoph Gorgulla, Süleyman Çınaroğlu, Patrick D. Fischer, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari |
VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization
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Special Issue Artificial Intelligence & Deep Learning Approaches for Structural Bioinformatics, 22(11), p. 5807, 2021 |
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2020
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Christoph Gorgulla, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari |
Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method
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Supercomputing Frontiers and Innovations, 7(3), pp. 4-12, 2020 |
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Christoph Gorgulla, Andras Boeszoermnyi, Zi-Fu Wang, Patrick D. Fischer, Paul Coote, Krishna M. Padmanabha Das, Yehor S. Malets, Dmytro S. Radchenko, Yurii Moroz, David A. Scott, Konstantin Fackeldey, Moritz Hoffmann, Iryna Iavniuk, Gerhard Wagner, Haribabu Arthanari |
An open-source drug discovery platform enables ultra-large virtual screens
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Nature, Vol.580, pp. 663-668, 2020 |
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2019
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Natalia Ernst, Konstantin Fackeldey, Andrea Volkamer, Oliver Opatz, Marcus Weber |
Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes
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Molecular Simulation, 45(11), pp. 904-911, 2019 |
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Konstantin Fackeldey, Peter Koltai, Peter Nevir, Henning Rust, Axel Schild, Marcus Weber |
From metastable to coherent sets - Time-discretization schemes
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Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol.29, pp. 012101-012101, 2019 (preprint available as ZIB-Report 17-74) |
PDF (ZIB-Report)
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Bernhard Reuter, Konstantin Fackeldey, Marcus Weber |
Generalized Markov modeling of nonreversible molecular kinetics
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The Journal of Chemical Physics, 17(150), p. 174103, 2019 |
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2018
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Bernhard Reuter, Marcus Weber, Konstantin Fackeldey, Susanna Röblitz, Martin E. Garcia |
Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field
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Journal of Chemical Theory and Computation, 14(7), pp. 3579-3594, 2018 |
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Jakob Witzig, Isabel Beckenbach, Leon Eifler, Konstantin Fackeldey, Ambros Gleixner, Andreas Grever, Marcus Weber |
Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes
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Multiscale Modeling and Simulation, 16(1), pp. 248-265, 2018 (preprint available as ZIB-Report 16-39) |
PDF (ZIB-Report)
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Konstantin Fackeldey, Alexander Sikorski, Marcus Weber |
Spectral Clustering for Non-Reversible Markov Chains
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Computational and Applied Mathematics, 37(5), pp. 6376-6391, 2018 (preprint available as ZIB-Report 18-48) |
PDF (ZIB-Report)
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2017
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Konstantin Fackeldey, Amir Niknejad, Marcus Weber |
Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation
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Special Matrices, pp. 73-81, 2017 |
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Konstantin Fackeldey, Marcus Weber |
GenPCCA -- Markov State Models for Non-Equilibrium Steady States
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Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29, pp. 70-80, 2017 |
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Marcus Weber, Konstantin Fackeldey, Christof Schütte |
Set-Free Markov State Model Building
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Journal of Chemical Physics, 146(12), 2017 (preprint available as ZIB-Report 17-10) |
PDF (ZIB-Report)
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DOI
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2015
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Konstantin Fackeldey
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Crossing the Scales in Structural Mechanics and Molecular Research
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Habilitation, Technische Universität Berlin, 2015 |
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Marcus Weber, Konstantin Fackeldey |
G-PCCA: Spectral Clustering for Non-reversible Markov Chains
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ZIB-Report 15-35 |
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2014
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Dorian Krause, Konstantin Fackeldey, Rolf Krause |
A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements
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Singular Phenomena and Scaling in Mathematical Models, pp. 327-346, 2014 (preprint available as ZIB-Report 13-50) |
PDF (ZIB-Report)
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Marcus Weber, Konstantin Fackeldey |
Computing the Minimal Rebinding Effect Included in a Given Kinetics
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Multiscale Model. Simul., 12(1), pp. 318-334, 2014 (preprint available as ZIB-Report 13-12) |
PDF (ZIB-Report)
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Karsten Andrae, Stefan Merkel, Vedat Durmaz, Konstantin Fackeldey, Robert Köppen, Marcus Weber, Matthias Koch |
Investigation of the Ergopeptide Epimerization Process
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Computation, 2(3), pp. 102-111, 2014 |
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Konstantin Fackeldey, Alexander Bujotzek |
Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach
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Progress in Industrial Mathematics at ECMI 2012, pp. 309-313, Vol.19, Mathematics in Industry, 2014 |
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Marcus Weber, Konstantin Fackeldey |
Local Refinements in Classical Molecular Dynamics Simulations
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J. Phys. Conf. Ser., Vol.490, p. 012016, 2014 |
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Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber |
ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling
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Journal of Mathematical Chemistry, 52(3), pp. 781-804, 2014 (preprint available as ZIB-Report 13-58) |
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2013
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Han Cheng Lie, Konstantin Fackeldey, Marcus Weber |
A Square Root Approximation of Transition Rates for a Markov State Model
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SIAM. J. Matrix Anal. Appl., 34(2), pp. 738-756, 2013 (preprint available as ZIB-Report 13-43) |
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Fiete Haack, Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber, Burkhard Schmidt |
Adaptive spectral clustering with application to tripeptide conformation analysis
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The Journal of Chemical Physics, Vol.139, pp. 110-194, 2013 |
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Olga Scharkoi, Konstantin Fackeldey, Igor Merkulow, Karsten Andrae, Marcus Weber, Irene Nehls |
Conformational Analysis of Alternariol on the Quantum Level
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J. Mol. Model., 19(6), pp. 2567-2572, 2013 |
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Karsten Andrae, Vedat Durmaz, Konstantin Fackeldey, Olga Scharkoi, Marcus Weber |
Medizin aus dem Computer
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Der Anaesthesist, 62(7), pp. 561-557, 2013 |
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Adam Nielsen, Konstantin Fackeldey, Marcus Weber |
On a Generalized Transfer Operator
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ZIB-Report 13-74 |
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2012
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Konstantin Fackeldey, Martina Klimm, Marcus Weber |
A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules
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Journal of Mathematical Chemistry, 5(9), pp. 2623-2635, 2012 |
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Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber |
A meshless discretization method for Markov state models applied to explicit water peptide folding simulations
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Meshfree Methods for Partial Differential Equations VI, pp. 141-154, Vol.89, Lecture Notes in Computational Science and Engineering, 2012 |
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Konstantin Fackeldey
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Multiscale Methods in Time and Space
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Progress in Industrial Mathematics at ECMI 2010, pp. 619-626, Vol.17, Mathematics in Industry, 2012 |
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2011
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Vedat Durmaz, Konstantin Fackeldey, Marcus Weber |
A rapidly Mixing Monte Carlo Method for the Simulation of Slow Molecular Processes
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Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science, Ch. Mode (Ed.), InTech, 2011 |
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Konstantin Fackeldey
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Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach
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IJPAM, 69(2), pp. 185-202, 2011 (preprint available as ZIB-Report 10-12) |
PDF (ZIB-Report)
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Konstantin Fackeldey, Dorian Krause, Rolf Krause, Christoph Lenzen |
Coupling Molecular Dynamics and Continua with Weak Constraints
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SIAM Multiscale Model. Simul., Vol.9, pp. 1459-1494, 2011 |
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Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber |
Soft Versus Hard Metastable Conformations in Molecular Simulations
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ZIB-Report 11-27 |
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URN
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2010
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Konstantin Fackeldey
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Challenges in Atomistic-to-Continuum Coupling
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(preprint available as ) |
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DOI
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Konstantin Fackeldey, Dorian Krause, Rolf Krause |
Numerical Validation of Constraints Based Multiscale Methods
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Lecture Notes in Computational Science and Engineering, Michael Griebel, M. Schweitzer (Eds.), pp. 141-154, 2010 |
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2009
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Konstantin Fackeldey, Rolf Krause |
Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics
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International Journal for Numerical Methods in Engineering, 79(12), pp. 1517-1535, 2009 |
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DOI
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Konstantin Fackeldey
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The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics
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Doctoral thesis, Institute for Numerical Simulation, Uni Bonn, 2009 |
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Konstantin Fackeldey, Dorian Krause, Rolf Krause |
Weak Coupling Algorithms in Multiscale Simulations
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Proceedings of the third Inter. Confer. on Comp. Meth. for Coupled Problems in
Science and Engrg, p. 1023pp, 2009 |
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2008
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Konstantin Fackeldey, Rolf Krause |
CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach
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Proc. Appl. Math. Mech., p. 10495pp, 8(1), 2008 |
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Konstantin Fackeldey, Dorian Krause, Rolf Krause |
Quadrature and Implementation of the Weak Coupling Method
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MMM 2008: Proceedings of the 4th International Conference on Multiscale Materials Modelling, 27-31 October 2008, Tallahassee, Fla., pp. 62-65, 2008 |
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Konstantin Fackeldey, Rolf Krause, M. Schweitzer |
Stability of Energy Transfer in the Weak Coupling Method
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Meshfree Methods for Partial Differential Equations IV, Michael Griebel, M. Schweitzer (Eds.), pp. 111-121, Vol.65, Lecture Notes in Computational Science and Engineering, 2008 |
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2007
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Konstantin Fackeldey, Rolf Krause |
Solving Frictional Contact Problems with Multigrid Efficiency
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Proc.of the 16th International Conference on Domain Decomposition Methods, Olof Widlund (Ed.), pp. 547-554, Vol.50, Lecture Notes in Computational Science and Engineering, 2007 |
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Konstantin Fackeldey, Rolf Krause |
Weak coupling in function space
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Proc. Appl. Math. Mech., p. 2020113pp, 7(1), 2007 |
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