2023
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	Biophysica, 3(2), pp. 263-275, 2023	BibTeX DOI
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	Journal of Cheminformatics, Vol.15, 2023	BibTeX DOI
Luca Donati, Konstantin Fackeldey, Marcus Weber	PLANTS+: Improving Ant Colony Algorithms for Drug Design	2023 (under review)	BibTeX DOI
2022
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	SIAM Journal on Multiscale Modeling and Simulation, 20(1), pp. 379-403, 2022	BibTeX arXiv DOI
Christoph Gorgulla, Abhilash Jayaraj, Konstantin Fackeldey, Haribabu Arthanari	Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches	Current Opinion in Chemical Biology, Vol.69, pp. 102156-102156-12, 2022	BibTeX DOI
N. Alexia Raharinirina, Konstantin Fackeldey, Marcus Weber	Qualitative Euclidean embedding of Disjoint Sets of Points	2022	BibTeX
Renata Sechi, Konstantin Fackeldey, Surahit Chewle, Marcus Weber	SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data	Algorithms, 15(9), p. 297, 2022	BibTeX DOI
2021
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	iScience, 24(2), p. 102021, 2021	BibTeX DOI
Konstantin Fackeldey, Jonas Röhm, Amir Niknejad, Surahit Chewle, Marcus Weber	Analyzing Raman Spectral Data without Separabiliy Assumption	Journal of Mathematical Chemistry, 3(59), pp. 575-596, 2021	BibTeX arXiv DOI
Susanne Röhl, Marcus Weber, Konstantin Fackeldey	Computing the minimal rebinding effect for non-reversible processes	Multiscale Modeling and Simulation, 19(1), pp. 460-477, 2021	BibTeX arXiv DOI
N. Alexia Raharinirina, Marcus Weber, Ralph Birk, Konstantin Fackeldey, Sarah M. Klasse, Tonio Sebastian Richter	Different Tools and Results for Correspondence Analysis	2021	BibTeX DOI
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	2021 (in progress)	BibTeX
Isabel Nitzke, Konstantin Fackeldey, Jadran Vrabec	Long range corrections for inhomogeneous fluids containing a droplet or a bubble	Molecular Simulation, pp. 1-14, 2021	BibTeX DOI
Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber	Neue Medikamente dank Supercomputern	Spektrum der Wissenschaft, pp. 40-46, 2021	BibTeX
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	Special Issue Artificial Intelligence & Deep Learning Approaches for Structural Bioinformatics, 22(11), p. 5807, 2021	BibTeX DOI
2020
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	Supercomputing Frontiers and Innovations, 7(3), pp. 4-12, 2020	BibTeX DOI
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	Nature, Vol.580, pp. 663-668, 2020	BibTeX DOI
2019
Natalia Ernst, Konstantin Fackeldey, Andrea Volkamer, Oliver Opatz, Marcus Weber	Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes	Molecular Simulation, 45(11), pp. 904-911, 2019	BibTeX DOI
Konstantin Fackeldey, Peter Koltai, Peter Nevir, Henning Rust, Axel Schild, Marcus Weber	From metastable to coherent sets - Time-discretization schemes	Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol.29, pp. 012101-012101, 2019 (preprint available as ZIB-Report 17-74)	PDF (ZIB-Report) BibTeX DOI
Bernhard Reuter, Konstantin Fackeldey, Marcus Weber	Generalized Markov modeling of nonreversible molecular kinetics	The Journal of Chemical Physics, 17(150), p. 174103, 2019	BibTeX DOI
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) BibTeX DOI
Konstantin Fackeldey, Alexander Sikorski, Marcus Weber	Spectral Clustering for Non-Reversible Markov Chains	Computational and Applied Mathematics, 37(5), pp. 6376-6391, 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, 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
Marcus Weber, Konstantin Fackeldey, Christof 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	Crossing the Scales in Structural Mechanics and Molecular Research	Habilitation, 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
Vedat Durmaz, Konstantin Fackeldey, Marcus 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
Konstantin 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
Konstantin Fackeldey	Challenges in Atomistic-to-Continuum Coupling	(preprint available as )	BibTeX DOI
Konstantin Fackeldey, Dorian Krause, Rolf Krause	Numerical Validation of Constraints Based Multiscale Methods	Lecture Notes in Computational Science and Engineering, Michael Griebel, M. Schweitzer (Eds.), pp. 141-154, 2010	BibTeX
2009
Konstantin Fackeldey, Rolf 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
Konstantin Fackeldey	The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics	Doctoral thesis, Institute for Numerical Simulation, Uni Bonn, 2009	BibTeX
Konstantin Fackeldey, Dorian Krause, Rolf 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
Konstantin Fackeldey, Rolf 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
Konstantin Fackeldey, Rolf Krause, M. Schweitzer	Stability of Energy Transfer in the Weak Coupling Method	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	BibTeX
2007
Konstantin Fackeldey, Rolf 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
Konstantin Fackeldey, Rolf Krause	Weak coupling in function space	Proc. Appl. Math. Mech., p. 2020113pp, 7(1), 2007	BibTeX