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Home Members Fackeldey, Konstantin, Priv. Doz. Dr.

Fackeldey, Konstantin, Priv. Doz. Dr.

Konstantin Fackeldey

Contact

Position
Head of Research Group
Room
4036
Phone
+49 30 84185-347
Email
Email
Website
Personal Homepage
Division
Mathematics of Complex Systems
Parallel and Distributed Computing
Department
Modeling and Simulation of Complex Processes
Supercomputing
Group
Computational Molecular Design
Efficient Large Scale Computing in Life Sciences

Projects

Projects as Head

HPC and Machine Learning for Drug Discovery

HPC and ML for Drug Discovery

High-performance computers are required to simulate complex systems that allow to study the behavior of molecules under real conditions. This project combines artificial...

HPC and ML for Drug Discovery
Pareto-ML-Optimization-Cycle

AA1-19 Drug Candidates as Pareto Optima in Chemical Space

The search for novel drug candidates that, at the same time, act with high efficacy, comply with defined chemical properties, and also show low off-target effects can be...

AA1-19 Drug Candidates as Pareto Optima in Chemical Space
Egytian

Ancient Egytian

The linguistic abilities of scribes writing in Egyptien de Tradition has been severely contested. The underlying assumptions on the evolutionary process of languages are...

Ancient Egytian
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Math-Powered Drug Design

This project aims at the creation of a MATH+ success story around the mathematics of drug design. It proposes a new drug design strategy for G-protein coupled receptors...

Math-Powered Drug Design

Projects as Member

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Cycle Detection in Nonreversible Markov Processes

The main objective of this project is to develop an adaptive sampling strategy for the identification of cycles in transition networks. To analyse transition networks...

Cycle Detection in Nonreversible Markov Processes
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Probing Scales in Equilibrated Systems by Optimal Nonequilibrium Forcing

The dynamics of biomolecules show an inherent multiscale behaviour with cascades of timescales and strong interaction between them. Molecular dynamics (MD) simulations...

Probing Scales in Equilibrated Systems by Optimal Nonequilibrium Forcing
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Investigation of the Ergoline Epimerization Process

We investigated six chemical agents of the group of alkaloid ergotamines. All substances are derivatives of lysergic acid. This kind of alkaloid can be found in fungi...

Investigation of the Ergoline Epimerization Process
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Modeling and Optimization of Functional Molecules

In this project we employ function space oriented methods for thermodynamical simulation and analysis of drug-like molecules. Based on a strong mathematical fundament we...

Modeling and Optimization of Functional Molecules

Publications

2024
A community effort in SARS-CoV-2 drug discovery Molecular Informatics, 43(1), p. e202300262, 2024 Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet-Melou, Ronan Bureau, Beatrice Charton, Bertrand C. Cirou, Gérard Gil, William J. Allen, Suman Sirimulla, Stanley Watowich, Nick Antonopoulos, Nikolaos Epitropakis, Agamemnon Krasoulis, Vassilis Itsikalis, Stavros Theodorakis, Igor Kozlovskii, Anton Maliutin, Alexander Medvedev, Petr Popov, Mark Zaretckii, Hamid Eghbal-Zadeh, Christina Halmich, Sepp Hochreiter, Andreas Mayr, Peter Ruch, Michael Widrich, Francois Berenger, Ashutosh Kumar, Yoshihiro Yamanishi, Kam Y. J. Zhang, Emmanuel Bengio, Yoshua Bengio, Moksh J. Jain, Maksym Korablyov, Cheng-Hao Liu, Gilles Marcou, Enrico Glaab, Kelly Barnsley, Suhasini M. Iyengar, Mary Jo Ondrechen, V. Joachim Haupt, Florian Kaiser, Michael Schroeder, Luisa Pugliese, Simone Albani, Christina Athanasiou, Andrea Beccari, Paolo Carloni, Giulia D’Arrigo, Eleonora Gianquinto, Jonas Goßen, Anton Hanke, Benjamin P. Joseph, Daria B. Kokh, Sandra Kovachka, Candida Manelfi, Goutam Mukherjee, Abraham Muñiz-Chicharro, Francesco Musiani, Ariane Nunes-Alves, Giulia Paiardi, Giulia Rossetti, S. Kashif Sadiq, Francesca Spyrakis, Carmine Talarico, Alexandros Tsengenes, Rebecca C. Wade, Conner Copeland, Jeremiah Gaiser, Daniel R. Olson, Amitava Roy, Vishwesh Venkatraman, Travis J. Wheeler, Haribabu Arthanari, Klara Blaschitz, Marco Cespugli, Vedat Durmaz, Konstantin Fackeldey, Patrick D. Fischer, Christoph Gorgulla, Christian Gruber, Karl Gruber, Michael Hetmann, Jamie E. Kinney, Krishna M. Padmanabha Das, Shreya Pandita, Amit Singh, Georg Steinkellner, Guilhem Tesseyre, Gerhard Wagner, Zi-Fu Wang, Ryan J. Yust, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Pavel V. Pogodin, Vladimir Poroikov, Anastassia V. Rudik, Leonid A. Stolbov, Alexander V. Veselovsky, Maria De Rosa, Giada De Simone, Maria R. Gulotta, Jessica Lombino, Nedra Mekni, Ugo Perricone, Arturo Casini, Amanda Embree, D. Benjamin Gordon, David Lei, Katelin Pratt, Christopher A. Voigt, Kuang-Yu Chen, Yves Jacob, Tim Krischuns, Pierre Lafaye, Agnès Zettor, M. Luis Rodríguez, Kris M. White, Daren Fearon, Frank Von Delft, Martin A. Walsh, Dragos Horvath, Charles L. Brooks III, Babak Falsafi, Bryan Ford, Adolfo García-Sastre, Sang Yup Lee, Nadia Naffakh, Alexandre Varnek, Günter Klambauer, Thomas M. Hermans BibTeX
DOI
Augmented ant colony algorithm for virtual drug discovery Journal of Mathematical Chemistry, Vol.62, pp. 367-385, 2024 Luca Donati, Konstantin Fackeldey, Marcus Weber BibTeX
DOI
Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables PLOS ONE, 19(5), 2024 Nomenjanahary Alexia Raharinirina, Vikram Sunkara, Max von Kleist, Konstantin Fackeldey, Marcus Weber BibTeX
DOI
2023
Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane Biophysica, 3(2), pp. 263-275, 2023 Sourav Ray, Konstantin Fackeldey, Christoph Stein, Marcus Weber BibTeX
DOI
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists Journal of Cheminformatics, Vol.15, 2023 Christopher Secker, Konstantin Fackeldey, Marcus Weber, Sourav Ray, Christoph Gorgulla, Christof Schütte BibTeX
DOI
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists (Dataset) 2023 Christopher Secker BibTeX
DOI
URN
VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules bioRxiv, 2023 (preprint available as ) Christoph Gorgulla, AkshatKumar Nigam, Matt Koop, Süleyman Selim Çınaroğlu, Christopher Secker, Mohammad Haddadnia, Abhishek Kumar, Yehor Malets, Alexander Hasson, Minkai Li, Ming Tang, Roni Levin-Konigsberg, Dmitry Radchenko, Aditya Kumar, Minko Gehev, Pierre-Yves Aquilanti, Henry Gabb, Amr Alhossary, Gerhard Wagner, Alán Aspuru-Guzik, Yurii S. Moroz, Konstantin Fackeldey, Haribabu Arthanari BibTeX
DOI
2022
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 Konstantin Fackeldey, Mathias Oster, Leon Sallandt, Reinhold Schneider BibTeX
arXiv
DOI
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 Christoph Gorgulla, Abhilash Jayaraj, Konstantin Fackeldey, Haribabu Arthanari BibTeX
DOI
Qualitative Euclidean embedding of Disjoint Sets of Points 2022 N. Alexia Raharinirina, Konstantin Fackeldey, Marcus Weber BibTeX
SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data Algorithms, 15(9), p. 297, 2022 Renata Sechi, Konstantin Fackeldey, Surahit Chewle, Marcus Weber BibTeX
DOI
2021
A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening iScience, 24(2), p. 102021, 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 BibTeX
DOI
Analyzing Raman Spectral Data without Separabiliy Assumption Journal of Mathematical Chemistry, 3(59), pp. 575-596, 2021 Konstantin Fackeldey, Jonas Röhm, Amir Niknejad, Surahit Chewle, Marcus Weber BibTeX
arXiv
DOI
Computing the minimal rebinding effect for non-reversible processes Multiscale Modeling and Simulation, 19(1), pp. 460-477, 2021 Susanne Röhl, Marcus Weber, Konstantin Fackeldey BibTeX
arXiv
DOI
Different Tools and Results for Correspondence Analysis 2021 N. Alexia Raharinirina, Marcus Weber, Ralph Birk, Konstantin Fackeldey, Sarah M. Klasse, Tonio Sebastian Richter BibTeX
DOI
Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts 2021 (in progress) Ralph Birk, N. Alexia Raharinirina, Konstantin Fackeldey, Tonio Sebastian Richter, Marcus Weber BibTeX
Long range corrections for inhomogeneous fluids containing a droplet or a bubble Molecular Simulation, pp. 1-14, 2021 Isabel Nitzke, Konstantin Fackeldey, Jadran Vrabec BibTeX
DOI
Neue Medikamente dank Supercomputern Spektrum der Wissenschaft, pp. 40-46, 2021 Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber BibTeX
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 Christoph Gorgulla, Süleyman Çınaroğlu, Patrick D. Fischer, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari BibTeX
DOI
2020
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 Christoph Gorgulla, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari BibTeX
DOI
An open-source drug discovery platform enables ultra-large virtual screens Nature, Vol.580, pp. 663-668, 2020 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 BibTeX
DOI
2019
Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes Molecular Simulation, 45(11), pp. 904-911, 2019 Natalia Ernst, Konstantin Fackeldey, Andrea Volkamer, Oliver Opatz, Marcus Weber BibTeX
DOI
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) Konstantin Fackeldey, Peter Koltai, Peter Nevir, Henning Rust, Axel Schild, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
Generalized Markov modeling of nonreversible molecular kinetics The Journal of Chemical Physics, 17(150), p. 174103, 2019 Bernhard Reuter, Konstantin Fackeldey, Marcus Weber BibTeX
DOI
2018
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 Bernhard Reuter, Marcus Weber, Konstantin Fackeldey, Susanna Röblitz, Martin E. Garcia BibTeX
DOI
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) Jakob Witzig, Isabel Beckenbach, Leon Eifler, Konstantin Fackeldey, Ambros Gleixner, Andreas Grever, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
Spectral Clustering for Non-Reversible Markov Chains Computational and Applied Mathematics, 37(5), pp. 6376-6391, 2018 (preprint available as ZIB-Report 18-48) Konstantin Fackeldey, Alexander Sikorski, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
2017
Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation Special Matrices, pp. 73-81, 2017 Konstantin Fackeldey, Amir Niknejad, Marcus Weber BibTeX
DOI
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 Konstantin Fackeldey, Marcus Weber BibTeX
DOI
Set-Free Markov State Model Building Journal of Chemical Physics, 146(12), 2017 (preprint available as ZIB-Report 17-10) Marcus Weber, Konstantin Fackeldey, Christof Schütte PDF (ZIB-Report)
BibTeX
DOI
2015
Crossing the Scales in Structural Mechanics and Molecular Research Habilitation, Technische Universität Berlin, 2015 Konstantin Fackeldey BibTeX
G-PCCA: Spectral Clustering for Non-reversible Markov Chains ZIB-Report 15-35 Marcus Weber, Konstantin Fackeldey PDF
BibTeX
URN
2014
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) Dorian Krause, Konstantin Fackeldey, Rolf Krause PDF (ZIB-Report)
BibTeX
DOI
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) Marcus Weber, Konstantin Fackeldey PDF (ZIB-Report)
BibTeX
DOI
Investigation of the Ergopeptide Epimerization Process Computation, 2(3), pp. 102-111, 2014 Karsten Andrae, Stefan Merkel, Vedat Durmaz, Konstantin Fackeldey, Robert Köppen, Marcus Weber, Matthias Koch BibTeX
DOI
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 Konstantin Fackeldey, Alexander Bujotzek BibTeX
DOI
Local Refinements in Classical Molecular Dynamics Simulations J. Phys. Conf. Ser., Vol.490, p. 012016, 2014 Marcus Weber, Konstantin Fackeldey PDF
BibTeX
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) Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
2013
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) Han Cheng Lie, Konstantin Fackeldey, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
Adaptive spectral clustering with application to tripeptide conformation analysis The Journal of Chemical Physics, Vol.139, pp. 110-194, 2013 Fiete Haack, Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber, Burkhard Schmidt BibTeX
DOI
Conformational Analysis of Alternariol on the Quantum Level J. Mol. Model., 19(6), pp. 2567-2572, 2013 Olga Scharkoi, Konstantin Fackeldey, Igor Merkulow, Karsten Andrae, Marcus Weber, Irene Nehls BibTeX
DOI
Medizin aus dem Computer Der Anaesthesist, 62(7), pp. 561-557, 2013 Karsten Andrae, Vedat Durmaz, Konstantin Fackeldey, Olga Scharkoi, Marcus Weber BibTeX
DOI
On a Generalized Transfer Operator ZIB-Report 13-74 Adam Nielsen, Konstantin Fackeldey, Marcus Weber PDF
BibTeX
URN
2012
A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules Journal of Mathematical Chemistry, 5(9), pp. 2623-2635, 2012 Konstantin Fackeldey, Martina Klimm, Marcus Weber BibTeX
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 Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber BibTeX
Multiscale Methods in Time and Space Progress in Industrial Mathematics at ECMI 2010, pp. 619-626, Vol.17, Mathematics in Industry, 2012 Konstantin Fackeldey BibTeX
2011
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 Vedat Durmaz, Konstantin Fackeldey, Marcus Weber BibTeX
Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach IJPAM, 69(2), pp. 185-202, 2011 (preprint available as ZIB-Report 10-12) Konstantin Fackeldey PDF (ZIB-Report)
BibTeX
Coupling Molecular Dynamics and Continua with Weak Constraints SIAM Multiscale Model. Simul., Vol.9, pp. 1459-1494, 2011 Konstantin Fackeldey, Dorian Krause, Rolf Krause, Christoph Lenzen BibTeX
DOI
Soft Versus Hard Metastable Conformations in Molecular Simulations ZIB-Report 11-27 Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber PDF
BibTeX
URN
2010
Challenges in Atomistic-to-Continuum Coupling (preprint available as ) Konstantin Fackeldey BibTeX
DOI
Numerical Validation of Constraints Based Multiscale Methods Lecture Notes in Computational Science and Engineering, Michael Griebel, M. Schweitzer (Eds.), pp. 141-154, 2010 Konstantin Fackeldey, Dorian Krause, Rolf Krause BibTeX
2009
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 Konstantin Fackeldey, Rolf Krause BibTeX
DOI
The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics Doctoral thesis, Institute for Numerical Simulation, Uni Bonn, 2009 Konstantin Fackeldey BibTeX
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 Konstantin Fackeldey, Dorian Krause, Rolf Krause BibTeX
2008
CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach Proc. Appl. Math. Mech., p. 10495pp, 8(1), 2008 Konstantin Fackeldey, Rolf Krause BibTeX
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 Konstantin Fackeldey, Dorian Krause, Rolf Krause BibTeX
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 Konstantin Fackeldey, Rolf Krause, M. Schweitzer BibTeX
2007
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 Konstantin Fackeldey, Rolf Krause BibTeX
Weak coupling in function space Proc. Appl. Math. Mech., p. 2020113pp, 7(1), 2007 Konstantin Fackeldey, Rolf Krause BibTeX