2018
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	Journal of Chemical Theory and Computation, 14(7), pp. 3579-3594, 2018	BibTeX DOI
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	Multiscale Modeling and Simulation, 16(1), pp. 248-265, 2018 (preprint available as ZIB-Report 16-39)	PDF (ZIB-Report) PDF (ZIB-Report) PDF (ZIB-Report) BibTeX DOI
Konstantin Fackeldey, Alexander Sikorski, Marcus Weber	Spectral Clustering for Non-Reversible Markov Chains	Computational and Applied Mathematics, pp. 1-16, 2018 (preprint available as ZIB-Report 18-48)	PDF (ZIB-Report) BibTeX DOI
2017
Konstantin Fackeldey, Amir Niknejad, Marcus Weber	Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation	Special Matrices, pp. 73-81, 2017	BibTeX DOI
Konstantin Fackeldey, Péter Koltai, Peter Névir, Henning Rust, Axel Schild, Marcus Weber	From Metastable to Coherent Sets - time-discretization schemes	ZIB-Report 17-74	PDF BibTeX URN
Konstantin Fackeldey, Marcus Weber	GenPCCA -- Markov State Models for Non-Equilibrium Steady States	Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29, pp. 70-80, 2017	BibTeX DOI
M. Weber, K. Fackeldey, Ch. Schütte	Set-Free Markov State Model Building	Journal of Chemical Physics, 146(12), 2017 (preprint available as ZIB-Report 17-10)	PDF (ZIB-Report) BibTeX DOI
2015
Konstantin Fackeldey	Challenges in Atomistic-to-Continuum Coupling	Mathematical Problems in Engineering, Vol.2015, 2015	BibTeX DOI
Konstantin Fackeldey	Crossing the Scales in Structural Mechanics and Molecular Research	Habilitation thesis, Technische Universität Berlin, 2015	BibTeX
Marcus Weber, Konstantin Fackeldey	G-PCCA: Spectral Clustering for Non-reversible Markov Chains	ZIB-Report 15-35	PDF BibTeX URN
2014
Dorian Krause, Konstantin Fackeldey, Rolf Krause	A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements	Singular Phenomena and Scaling in Mathematical Models, pp. 327-346, 2014 (preprint available as ZIB-Report 13-50)	PDF (ZIB-Report) BibTeX DOI
Marcus Weber, Konstantin Fackeldey	Computing the Minimal Rebinding Effect Included in a Given Kinetics	Multiscale Model. Simul., 12(1), pp. 318-334, 2014 (preprint available as ZIB-Report 13-12)	PDF (ZIB-Report) BibTeX DOI
Karsten Andrae, Stefan Merkel, Vedat Durmaz, Konstantin Fackeldey, Robert Köppen, Marcus Weber, Matthias Koch	Investigation of the Ergopeptide Epimerization Process	Computation, 2(3), pp. 102-111, 2014	BibTeX DOI
Konstantin Fackeldey, Alexander Bujotzek	Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach	Progress in Industrial Mathematics at ECMI 2012, pp. 309-313, Vol.19, Mathematics in Industry, 2014	BibTeX DOI
Marcus Weber, Konstantin Fackeldey	Local Refinements in Classical Molecular Dynamics Simulations	J. Phys. Conf. Ser., Vol.490, p. 012016, 2014	PDF BibTeX
Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber	ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling	Journal of Mathematical Chemistry, 52(3), pp. 781-804, 2014 (preprint available as ZIB-Report 13-58)	PDF (ZIB-Report) BibTeX DOI
2013
Han Cheng Lie, Konstantin Fackeldey, Marcus Weber	A Square Root Approximation of Transition Rates for a Markov State Model	SIAM. J. Matrix Anal. Appl., 34(2), pp. 738-756, 2013 (preprint available as ZIB-Report 13-43)	PDF (ZIB-Report) BibTeX DOI
Fiete Haack, Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber, Burkhard Schmidt	Adaptive spectral clustering with application to tripeptide conformation analysis	The Journal of Chemical Physics, Vol.139, pp. 110-194, 2013	BibTeX DOI
Olga Scharkoi, Konstantin Fackeldey, Igor Merkulow, Karsten Andrae, Marcus Weber, Irene Nehls	Conformational Analysis of Alternariol on the Quantum Level	J. Mol. Model., 19(6), pp. 2567-2572, 2013	BibTeX DOI
Karsten Andrae, Vedat Durmaz, Konstantin Fackeldey, Olga Scharkoi, Marcus Weber	Medizin aus dem Computer	Der Anaesthesist, 62(7), pp. 561-557, 2013	BibTeX DOI
Adam Nielsen, Konstantin Fackeldey, Marcus Weber	On a Generalized Transfer Operator	ZIB-Report 13-74	PDF BibTeX URN
2012
Konstantin Fackeldey, Martina Klimm, Marcus Weber	A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules	Journal of Mathematical Chemistry, 5(9), pp. 2623-2635, 2012	BibTeX
Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber	A meshless discretization method for Markov state models applied to explicit water peptide folding simulations	Meshfree Methods for Partial Differential Equations VI, pp. 141-154, Vol.89, Lecture Notes in Computational Science and Engineering, 2012	BibTeX
Konstantin Fackeldey	Multiscale Methods in Time and Space	Progress in Industrial Mathematics at ECMI 2010, pp. 619-626, Vol.17, Mathematics in Industry, 2012	BibTeX
2011
V. Durmaz, K. Fackeldey, M. Weber	A rapidly Mixing Monte Carlo Method for the Simulation of Slow Molecular Processes	Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science, Ch. Mode (Ed.), InTech, 2011	BibTeX
K. Fackeldey	Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach	IJPAM, 69(2), pp. 185-202, 2011 (preprint available as ZIB-Report 10-12)	PDF (ZIB-Report) BibTeX
Konstantin Fackeldey, Dorian Krause, Rolf Krause, Christoph Lenzen	Coupling Molecular Dynamics and Continua with Weak Constraints	SIAM Multiscale Model. Simul., Vol.9, pp. 1459-1494, 2011	BibTeX DOI
Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber	Soft Versus Hard Metastable Conformations in Molecular Simulations	ZIB-Report 11-27	PDF BibTeX URN
2010
K. Fackeldey, D. Krause, R. Krause	Numerical Validation of Constraints Based Multiscale Methods	Lecture Notes in Computational Science and Engineering, M. Griebel, M. Schweitzer (Eds.), pp. 141-154, 2010	BibTeX
2009
K. Fackeldey, R. Krause	Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics	International Journal for Numerical Methods in Engineering, 79(12), pp. 1517-1535, 2009	BibTeX DOI
K. Fackeldey	The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics	Doctoral thesis, Institute for Numerical Simulation, Uni Bonn, 2009	BibTeX
K. Fackeldey, D. Krause, R. Krause	Weak Coupling Algorithms in Multiscale Simulations	Proceedings of the third Inter. Confer. on Comp. Meth. for Coupled Problems in Science and Engrg, p. 1023pp, 2009	BibTeX
2008
K. Fackeldey, R. Krause	CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach	Proc. Appl. Math. Mech., p. 10495pp, 8(1), 2008	BibTeX
Konstantin Fackeldey, Dorian Krause, Rolf Krause	Quadrature and Implementation of the Weak Coupling Method	MMM 2008: Proceedings of the 4th International Conference on Multiscale Materials Modelling, 27-31 October 2008, Tallahassee, Fla., pp. 62-65, 2008	BibTeX
K. Fackeldey, R. Krause, M. Schweitzer	Stability of Energy Transfer in the Weak Coupling Method	Meshfree Methods for Partial Differential Equations IV, M. Griebel, M. Schweitzer (Eds.), pp. 111-121, Vol.65, Lecture Notes in Computational Science and Engineering, 2008	BibTeX
2007
K. Fackeldey, R. Krause	Solving Frictional Contact Problems with Multigrid Efficiency	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	BibTeX
K. Fackeldey, R. Krause	Weak coupling in function space	Proc. Appl. Math. Mech., p. 2020113pp, 7(1), 2007	BibTeX