Weber, Marcus, PD Dr.

Kontakt

Position

Leitung Arbeitsgruppe

Raum

4023

Telefon

+49 30 84185-189

E-Mail

Website

https://www.zib.de/userpage/weber/

Projekte

Projekte als Leitung

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

Mathematical Research Data Initiative - TA4

The Mathematics Research Data Initiative (MaRDI) is one of the consortia within the National Research Data Infrastructure (NFDI). It aims to make mathematical research...

Mathematical Research Data Initiative - TA4

The spatio-temporal modelling of mechanisms underlying pain relief via the µ-opioid receptor

We model all different aspects of μ-opioid receptor activation. This starts with the binding of an opioid to the receptor, followed by conformnational changes, spatio...

The spatio-temporal modelling of mechanisms underlying pain relief via the µ-opioid receptor

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

Publikationen

2025

A Case Study of the Use of Logical Data Analysis in the Workmen’s Village in Tell el-Amarna, Egypt it - Information Technology, 66(6), pp. 256-268, 2025 Sarah Michelle Klasse, Marcus Weber BibTeX
DOI

Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023, 2025 Alexander Sikorski, Robert Julian Rabben, Surahit Chewle, Marcus Weber BibTeX
arXiv
DOI

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition BMC Bioinformatics, 26(147), 2025 Maryam Yousefian, Anne-Simone Frank, Marcus Weber, Susanna Röblitz BibTeX
DOI

Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN 23rd International Conference on Computational Methods in Systems Biology, CMSB 2025, 2025 (accepted for publication) Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber, Susanna Röblitz BibTeX

2024

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

Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN Journal of Mathematical Physics, Vol.65, p. 013502, 2024 Alexander Sikorski, Enric Ribera Borrell, Marcus Weber BibTeX
arXiv
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

Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies Journal of Chemical Physics, Vol.160, p. 104112, 2024 Alexander Sikorski, Amir Niknejad, Marcus Weber, Luca Donati BibTeX
arXiv
DOI

The Kramers turnover in terms of a macro-state projection on phase space Molecular Physics, p. e2356748, 2024 (epub ahead of print) Luca Donati, Christof Schütte, Marcus Weber BibTeX
DOI

Topological analysis reveals multiple pathways in molecular dynamics 2024 (under review) Luca Donati, Surahit Chewle, Dominik St. Pierre, Vijay Natarajan, Marcus Weber BibTeX
arXiv

Towards a FAIR Documentation of Workflows and Models in Applied Mathematics Mathematical Software – ICMS 2024, pp. 254-262, Vol.14749, 2024 Marco Reidelbach, Björn Schembera, Marcus Weber BibTeX
arXiv
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

Efficient Estimation of Transition Rates as Functions of pH Proceedings in Applied Mathematics & Mechanics, Vol.23, 2023 (epub ahead of print) Luca Donati, Marcus Weber BibTeX
arXiv
DOI

Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen DWA-Themen, Vol.T1/2023, DWA, 2023 Thomas Ternes, Karl-Heinz Bauer, Frank Brauer, Jürgen Drewes, Kevin Jewell, Adriano Joss, Jörg Oehlmann, Michael Radtke, Ulrike Schulte-Oehlmann, Thomas Schwartz, Peter Seel, Jeanette Völker, Lilo Weber, Marcus Weber BibTeX

Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen Christian Wilhelm (Ed.), DWA / GDCh, 2023, ISBN: 978-3-96862-563-8 Thomas Ternes, Karl-Heinz Bauer, Frank Brauer, Jörg Drewes, Adriano Joss, Georg Hiller, Kevin Jewell, Jörg Oehlmann, Michael Radke, Ulrike Schulte-Oehlmann, Thomas Schwartz, Peter Seel, Jeanette Völker, Lilo Weber, Marcus Weber BibTeX

MaRDMO Plugin Proceedings of the Conference on Research Data Infrastructure, Vol.1, 2023 Marco Reidelbach, Eloi Ferrer, Marcus Weber BibTeX
DOI

Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design Scientific Reports, 13(607), 2023 Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann 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

Research-Data Management Planning in the German Mathematical Community Eur. Math. Soc. Mag., Vol.130, pp. 40-47, 2023 (epub ahead of print) Tobias Boege, René Fritze, Christiane Görgen, Jeroen Hanselmann, Dorothea Iglezakis, Lars Kastner, Thomas Koprucki, Tabea Krause, Christoph Lehrenfeld, Silvia Polla, Marco Reidelbach, Christian Riedel, Jens Saak, Björn Schembera, Karsten Tabelow, Marcus Weber BibTeX
DOI

Revealing Kinetics of Paracetamol Crystallization Using Time-Resolved Raman Spectroscopy, Orthogonal Time-Lapse Photography, and Non-Negative Matrix Factorization (OSANO) Crystal Growth & Design, 23(9), pp. 6737-6746, 2023 Surahit Chewle, Marcus Weber, Franziska Emmerling BibTeX
DOI

2022

A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models Journal of Mathematical Physics, 63(12), pp. 123306-1-123306-21, 2022 Luca Donati, Marcus Weber, Bettina G. Keller BibTeX
DOI

Assessing transition rates as functions of environmental variables The Journal of Chemical Physics, 157(22), pp. 224103-1-224103-14, 2022 Luca Donati, Marcus Weber BibTeX
DOI

Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension SIAM Journal on Numerical Analysis, 2022 (under review) Martin Heida, Alexander Sikorski, Marcus Weber BibTeX
DOI

Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures Angewandte Chemie, 61(48), p. e202208647, 2022 Rita Fernandes, Suvrat Chaowdhary, Noureldin Saleh, Natalia Mikula, Katerina Kanevche, Hans Berlepsch, Naoki Hosogi, Joachim Heberle, Marcus Weber, Christoph Böttcher, Beate Koksch BibTeX

Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative) GAMM Rundbrief, pp. 40-43, 2022 Peter Benner, Michael Burger, Dominik Göddeke, Christiane Görgen, Christian Himpe, Jan Heiland, Thomas Koprucki, Mario Ohlberger, Stephan Rave, Marco Reidelbach, Jens Saak, Anita Schöbel, Karsten Tabelow, Marcus Weber BibTeX

MaRDI - The mathematical Research Data Initiative Aktionstag Forschungsdaten, 2022 Marco Reidelbach, Marcus Weber BibTeX
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Parameter estimation on multivalent ITC data sets Scientific Reports, Vol.12, p. 13402, 2022 Franziska Erlekam, Maximilian Zumbansen, Marcus Weber BibTeX
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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

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

Estimation of the Koopman Generator by Newton's Extrapolation Multiscale Modeling and Simulation, 19(2), pp. 758-774, 2021 Renata Sechi, Alexander Sikorski, Marcus Weber 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

MSM building and projection for the analysis of time-resolved spectra Proceedings in Applied Mathematics and Mechanics, p. e202100102, 2021 Renata Sechi, Marcus Weber, Karsten Heyne BibTeX
DOI
URN

Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux Journal of Physics: Condensed Matter, 33(11), p. 115902, 2021 Luca Donati, Marcus Weber, Bettina G. Keller BibTeX
DOI

Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design ZIB-Report 21-19 Sourav Ray, Arne Thies, Vikram Sunkara, Hanna Wulkow, Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann PDF
BibTeX
URN

Neue Medikamente dank Supercomputern Spektrum der Wissenschaft, pp. 40-46, 2021 Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber BibTeX

Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection Viruses, 13(12), p. 2456, 2021 Wolfgang Bauer, Marcus Weber, Eva Diehl-Wiesenecker, Noa Galtung, Monika Prpic, Rajan Somasundaram, Rudolf Tauber, Jochen Schwenk, Patrick Micke, Kai Kappert BibTeX
DOI

The Augmented Jump Chain Advanced Theory and Simulations, 4(4), 2021 Alexander Sikorski, Marcus Weber, Christof Schütte BibTeX
arXiv
DOI

2020

DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten Beuth Verlag, 2020 Marcus Weber, Weitere Autoren BibTeX

Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study Crystals, 10(12), p. 1107, 2020 Surahit Chewle, Franziska Emmerling, Marcus Weber BibTeX
DOI

How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs Molecular Simulation, 46(18), pp. 1443-1452, 2020 (preprint available as ZIB-Report 20-18) Sourav Ray, Vikram Sunkara, Christof Schütte, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI

ISOKANN: Invariant subspaces of Koopman operators learned by a neural network The Journal of Chemical Physics, 153(11), p. 114109, 2020 Robert Julian Rabben, Sourav Ray, Marcus Weber BibTeX
DOI

Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities Analytical and Bioanalytical Chemistry, Vol.412, pp. 5247-5260, 2020 José Villatoro, Martin Zühlke, Daniel Riebe, Toralf Beitz, Marcus Weber, Hans-Gerd Löhmannsröben 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
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Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC Computation, 7(3), p. 46, 2019 Franziska Erlekam, Sinaida Igde, Susanna Röblitz, Laura Hartmann, Marcus Weber BibTeX
DOI

Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces Advanced Materials Interfaces, 6(13), p. 1900501, 2019 Narendra Lagumaddepalli Venkatareddy, Patrick Wilke, Natalia Ernst, Justus Horch, Marcus Weber, Andre Dallmann, Hans G. Börner BibTeX
DOI

Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations International Journal of Mass Spectrometry, Vol.436, pp. 108-117, 2019 José Villatoro, Marcus Weber, Martin Zühlke, Andreas Lehmann, Karl Zechiowski, Daniel Riebe, Toralf Beitz, Hans-Gerd Löhmannsröben, Oliver Kreuzer BibTeX
DOI

Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung KA Korrespondenz Abwasser, Abfall, Vol.7, pp. 551-557, 2019 Marcus Weber BibTeX

What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays Water Research, Vol.152, pp. 47-60, 2019 Aennes Abbas, Ilona Schneider, Anna Bollmann, Jan Funke, Jörg Oehlmann, Carsten Prasse, Ulrike Schulte-Oehlmann, Wolfram Seitz, Thomas Ternes, Marcus Weber, Henning Wesely, Martin Wagner BibTeX
DOI

pKa of opioid ligands as a discriminating factor for side effects Scientific Reports, Vol.9, p. 19344, 2019 Giovanna Del Vecchio, Dominika Labuz, Julia Temp, Viola Seitz, Michael Kloner, Roger Negrete, Antonio Rodriguez-Gaztelumendi, Marcus Weber, Halina Machelska, Christoph Stein BibTeX
DOI

2018

An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells PLOS ONE, 13(1), pp. e0191423-e0191423, 2018 Katharina Schrade, Jessica Tröger, Adeep Eldashan, Kerstin Zühlke, Kamal R. Abdul Azees, Jonathan M. Elkins, Martin Neuenschwander, Andreas Oder, Mohamed Elkewedi, Sarah Jaksch, Karsten Andrae, Jinliang Li, Jaoa Fernandes, Paul Markus Müller, Stephan Grunwald, Stephen F. Marino, Tanja Vukicevic, Jenny Eichhorst, Burkhard Wiesner, Marcus Weber, Michael Kapiloff, Oliver Rocks, Oliver Daumke, Thomas Wieland, Stefan Knapp, Jens Peter von Kries, Enno Klussmann BibTeX
DOI

An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates SIAM Journal on Scientific Computing, 40(2), pp. A653-A670, 2018 (preprint available as ZIB-Report 17-09) Jannes Quer, Luca Donati, Bettina Keller, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI

Estimation of the infinitesimal generator by square-root approximation J. Phys.: Condens. Matter, 30(42), pp. 425201-425201, 2018 Luca Donati, Martin Heida, Bettina G. Keller, Marcus Weber BibTeX
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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

Implications of PCCA+ in Molecular Simulation Computation, 6(1), p. 20, 2018 Marcus Weber BibTeX
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Mathematical modeling of the spreading of innovations in the ancient world eTopoi. Journal for Ancient Studies, Vol.7, 2018 Natasa Djurdjevac Conrad, Daniel Fuerstenau, Ana Grabundzija, Luzie Helfmann, Martin Park, Wolfram Schier, Brigitta Schütt, Christof Schütte, Marcus Weber, Niklas Wulkow, Johannes Zonker PDF
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

Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist Scientific Reports, Vol.8, p. 8965, 2018 Viola Spahn, Giovanna Del Vecchio, Antonio Rodriguez-Gaztelumendi, Julia Temp, Dominika Labuz, Michael Kloner, Marco Reidelbach, Halina Machelska, Marcus Weber, Christoph Stein BibTeX

Prediction of perturbed proton transfer networks PLoS ONE, 13(12), pp. e0207718-e0207718, 2018 Marco Reidelbach, Marcus Weber, Petra Imhof BibTeX
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Role of Counterions in Molecularly Imprinted Polymers for Anionic Species Langmuir, 34(23), pp. 6963-6975, 2018 Sabine Wagner, Carlos Zapata, Wei Wan, Kornelia Gawlitza, Marcus Weber, Knut Rurack 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

Supplementary: Implications of PCCA+ in Molecular Simulation 2018 Marcus Weber BibTeX

Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung KA Korrespondenz Abwasser, Abfall, 2018 (accepted for publication) Marcus Weber BibTeX

2017

A nontoxic pain killer designed by modeling of pathological receptor conformations Science, 355(6328), pp. 966-969, 2017 Viola Spahn, Giovanna Del Vecchio, Dominika Labuz, Antonio Rodriguez-Gaztelumendi, N. Massaly, Julia Temp, Vedat Durmaz, P. Sabri, Marco Reidelbach, Halina Machelska, Marcus Weber, Christoph Stein BibTeX
DOI

Eigenvalues of non-reversible Markov chains – A case study ZIB-Report 17-13 Marcus Weber PDF
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URN

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
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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
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Importance sampling in path space for diffusion processes with slow-fast variables Probability Theory and Related Fields, pp. 1-52, 2017 Carsten Hartmann, Christof Schütte, Marcus Weber, Wei Zhang BibTeX
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Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH Marcomolecular Bioscience, 17(12), p. 1700198, 2017 Sinaida Igde, Susanna Röblitz, Anne Müller, Katharina Kolbe, Sophia Boden, Claudia Fessele, Thisbe Lindhorst, Marcus Weber, Laura Hartmann BibTeX
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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)
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Supplementary simulation data for Science Manuscript ai8636 2017 Marcus Weber, Vedat Durmaz, Peggy Sabri, Marco Reidelbach BibTeX
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2016

Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements Chem. Eur. J., 22(43), pp. 15475-15484, 2016 Larissa K. S. Krebek, von, Andreas J. Achazi, Marthe Solleder, Marcus Weber, Beate Paulus, Christoph A. Schalley BibTeX
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Finding dominant structures of nonreversible Markov processes Multiscale Modeling and Simulation, 14(4), pp. 1319-1340, 2016 (preprint available as ZIB-Report 15-40) Natasa Djurdjevac Conrad, Marcus Weber, Christof Schütte PDF (ZIB-Report)
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IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector International Journal for Ion Mobility Spectrometry, pp. 197-297, 2016 José Villatoro, Martin Zühlke, Daniel Riebe, Toralf Beitz, Marcus Weber, Jens Riedel, Hans-Gerd Löhmannsröben BibTeX
DOI

2015

Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix KA Korrespondenz Abwasser, Abfall, Vol.3/15, pp. 264-267, 2015 Vedat Durmaz, Marcus Weber, Meyer, Mückter BibTeX

Computing the nearest reversible Markov chain Numerical Linear Algebra with Applications, 22(3), pp. 483-499, 2015 (preprint available as ZIB-Report 14-48) Adam Nielsen, Marcus Weber PDF (ZIB-Report)
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DOI

Estimating exit rates in rare event dynamical systems via extrapolation ZIB-Report 15-54 Marcus Weber, Jannes Quer PDF
PDF
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URN

G-PCCA: Spectral Clustering for Non-reversible Markov Chains ZIB-Report 15-35 Marcus Weber, Konstantin Fackeldey PDF
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High affinity flourescence labelled ligands for the estrogen receptor Eur. J. Org. Chem., 2015(10), pp. 2157-2166, 2015 Frank Abendroth, Marthe Solleder, Pia Welker, Kai Licha, Marcus Weber, Oliver Seitz, Dorothea Mangoldt BibTeX

Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015, 2015 Sinaida Igde, Hendrik Wölk, Susanna Röblitz, Marco Reidelbach, Marcus Weber, Laura Hartmann BibTeX

Markov State Models and Molecular Alchemy Molecular Physics, 113(1), pp. 69-78, 2015 (preprint available as ZIB-Report 14-05) Christof Schütte, Adam Nielsen, Marcus Weber PDF (ZIB-Report)
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Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands Beilstein J. Org. Chem., Vol.11, pp. 837-847, 2015 Koschek, Vedat Durmaz, Krylova, Wieczorek, Pooja Gupta, Richter, Alexander Bujotzek, Fischer, Rainer Haag, Freund, Marcus Weber, Rademann BibTeX

2014

Applications of the cross-entropy method to importance sampling and optimal control of diffusions Siam Journal on Scientific Computing, 36(6), pp. A2654-A2672, 2014 (preprint available as ZIB-Report 14-10) Wei Zhang, Han Wang, Carsten Hartmann, Marcus Weber, Christof Schütte PDF (ZIB-Report)
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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)
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Design of functional molecules MATHEON-Mathematics for Key Technologies, Vol.1, pp. 49-65, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Ulrich Horst, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Christof Schütte, Martin Skutella, Jürgen Sprekels (Eds.), European Mathematical Society, 2014 Christof Schütte, Peter Deuflhard, Frank Noé, Marcus Weber BibTeX

Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters J Nanomed Nanotechnol, 5(5), p. 234, 2014 Marcus Weber, Christian Zoschke, Amir Sedighi, Emanuel Fleige, Rainer Haag, Monika Schäfer-Korting BibTeX
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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
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Local Refinements in Classical Molecular Dynamics Simulations J. Phys. Conf. Ser., Vol.490, p. 012016, 2014 Marcus Weber, Konstantin Fackeldey PDF
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Mathematics without pain MATHEON-Mathematics for Key Technologies, Vol.1, pp. 26-28, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Ulrich Horst, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Martin Skutella, Jürgen Sprekels (Eds.), European Mathematical Society, 2014 Peter Deuflhard, Marcus Weber BibTeX
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Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane Molecular Simulation, 2014 Olga Scharkoi, Susanne Esslinger, Roland Becker, Marcus Weber, Irene Nehls BibTeX
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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)
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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)
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A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens Journal of Chemical Information and Modeling, 53(10), pp. 2681-2688, 2013 Vedat Durmaz, Sebastian Schmidt, Peggy Sabri, Christian Piechotta, Marcus Weber PDF
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Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series, pp. 147-157, 2013 Marcus Weber BibTeX

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
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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
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Fentanyl derivatives as pH-dependent opioid receptor agonists European Patent Application, Bulletin 2013/08, 2013 Christoph Stein, Marcus Weber, Christian Zöllner, Olga Scharkoi PDF
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Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification Advances in Data Analysis and Classification, 7(2), pp. 147-179, 2013 Susanna Röblitz, Marcus Weber BibTeX
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Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles J. Phys. Chem. C, 117(23), pp. 12307-12317, 2013 Rahul Tyagi, Shashwat Malhotra, Andreas F. Thünemann, Amir Sedighi, Marcus Weber, Andreas Schäfer, Rainer Haag BibTeX

Medizin aus dem Computer Der Anaesthesist, 62(7), pp. 561-557, 2013 Karsten Andrae, Vedat Durmaz, Konstantin Fackeldey, Olga Scharkoi, Marcus Weber BibTeX
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Method and system for identifying compounds that bind and preferably activate a target opioid receptor in a pH-dependent manner European Patent Application, Bulletin 2013/28, 2013 Christoph Stein, Marcus Weber, Olga Scharkoi, Peter Deuflhard PDF
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Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor ACS Chem. Biol., 8(4), pp. 707-715, 2013 Min Shan, Kathryn E. Carlson, Alexander Bujotzek, Anja Wellner, Ronald Gust, Marcus Weber, John A. Katzenellenbogen, Rainer Haag PDF
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On a Generalized Transfer Operator ZIB-Report 13-74 Adam Nielsen, Konstantin Fackeldey, Marcus Weber PDF
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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

Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration ZIB-Report 12-35 Burcu Tunga, Marcus Weber PDF
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How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers Journal of Molecular Modeling, Vol.18, pp. 2399-2408, 2012 Vedat Durmaz, Marcus Weber, Roland Becker BibTeX
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Multivalency as a Chemical Organization and Action Principle Angew. Chem. Int. Ed., 51(42), pp. 10472-10498, 2012 Carlo Fasting, Christoph A. Schalley, Marcus Weber, Oliver Seitz, Stefan Hecht, Beate Koksch, Jens Dernedde, Christina Graf, Ernst-Walter Knapp, Rainer Haag BibTeX

Photochemical trans-/cis-isomerization and quantification of zearalenone in edible oils J. Agric. Food Chem., Vol.60, pp. 11733-11740, 2012 Robert Köppen, Juliane Riedel, Matthias Proske, Sarah Drzymala, Tatjana Rasenko, Vedat Durmaz, Marcus Weber, Matthias Koch BibTeX
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Quantifying the rebinding effect in multivalent chemical ligand-receptor systems J. Chem. Phys., 137(5), p. 054111, 2012 Marcus Weber, Alexander Bujotzek, Rainer Haag BibTeX

The funnel trap paradox ZIB-Report 12-12 Marcus Weber PDF
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2011

A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator Habilitation, Freie Universität Berlin, 2011 Marcus Weber PDF
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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

Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces J. Mol. Sim., 2011 Marcus Weber, Alexander Bujotzek, Karsten Andrae, M. Weinhart, Rainer Haag BibTeX

Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding ChemBioChem, 12(17), pp. 2587-2598, 2011 Min Shan, Alexander Bujotzek, Frank Abendroth, Oliver Seitz, Marcus Weber, Rainer Haag BibTeX
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DNA-controlled bivalent presentation of ligands for the estrogen receptor Angew. Chem. Int. Ed., 2011 Frank Abendroth, Alexander Bujotzek, Min Shan, Rainer Haag, Marcus Weber, Oliver Seitz BibTeX

DNA-programmed spatial screening of carbohydrate-lectin interactions Chem. Sci., Vol.2, pp. 770-775, 2011 Ch. Scheibe, Alexander Bujotzek, Jens Dernedde, Marcus Weber, O. Seitz BibTeX

Direct Reweighting Strategies in Conformation Dynamics MATCH Commun. Math. Comp. Chem., Vol.65(2), pp. 333-346, 2011 Martina Klimm, Alexander Bujotzek, Marcus Weber BibTeX

Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites Organohalogen Compounds, Vol.73, pp. 730-733, 2011 O. Scharkoi, Susanne Esslinger, Roland Becker, Marcus Weber, Irene Nehls PDF
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Soft Versus Hard Metastable Conformations in Molecular Simulations Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.), pp. 899-909, 2011 (preprint available as ZIB-Report 11-27) Konstantin Fackeldey, Susanna Röblitz, O. Scharkoi, Marcus Weber PDF (ZIB-Report)
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Towards a rational spacer design for bivalent inhibition of estrogen receptor J. Comput.-Aided Mol. Des., Vol.25(3), pp. 253-262, 2011 Alexander Bujotzek, Min Shan, Rainer Haag, Marcus Weber BibTeX

2010

A simple method for the estimation of entropy differences MATCH Commun. Math. Comp. Chem. 2010, Vol.63(2), pp. 319-332, 2010 Marcus Weber, Karsten Andrae BibTeX

Adaptive Spectral Clustering for Conformation Analysis AIP Conference Proceedings, 1281(1), pp. 1585-1588, 2010 Fiete Haack, Susanna Röblitz, Olga Scharkoi, Burkhard Schmidt, Marcus Weber BibTeX
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Dynamic covalent hydrazine chemistry as a specific extraction and cleanup technique for the quantification of the Fusarium mycotoxin zearalenone in edible oils Journal of Chromatography A, Vol.1217(15), pp. 2206-15, 2010 D. Siegel, Karsten Andrae, Matthias Proske, C. Kochan, Matthias Koch, Marcus Weber, Irene Nehls BibTeX

Handlungsmöglichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren Rückständen in das Roh- und Trinkwasser. H.H. Dieter, K. Götz, K. Kümmerer, B. Rechenberg, F. Keil (Eds.), Umweltbundesamt, 2010 H. H. Dieter, K. Götz, K. Kümmerer, B. Rechenberg, F. Keil PDF
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Observation uncertainty in reversible Markov chains Phys. Rev. E, 82(3), p. 031114, 2010 Ph. Metzner, Marcus Weber, Christof Schütte BibTeX
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2009

A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator ZIB-Report 09-27 Marcus Weber PDF
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Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach Journal of Bioinformatics and Computational Biology, Vol.7(5), pp. 811-831, 2009 Alexander Bujotzek, Marcus Weber BibTeX

Fuzzy Spectral Clustering by PCCA+ Classification and Clustering: Models, Software and Applications, pp. 73-79, 2009 Susanna Röblitz, Marcus Weber BibTeX

HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota Organohalogen Compounds, Vol.70, pp. 910-913, 2009 Robert Köppen, Roland Becker, Marcus Weber, Vedat Durmaz, Irene Nehls BibTeX

Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR Organohalogen Compounds, Vol.71, pp. 247-252, 2009 Marcus Weber, Vedat Durmaz, Roland Becker, Susanne Esslinger BibTeX

Spurenstoffe im Trinkwasser - Risikoqualifizierung im Rechner? Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, L. Dunemann, O. Schmoll (Eds.), 2009 Marcus Weber BibTeX

2008

An efficient analysis of rare events in canonical ensemble dynamics ZIB-Report 08-36 Marcus Weber PDF
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Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane Journal of Molecular Simulation, 34(7), pp. 727-736, 2008 (preprint available as ZIB-Report 07-31) Marcus Weber, Roland Becker, Robert Köppen, Vedat Durmaz PDF (ZIB-Report)
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Computation of equilibrium densities in metastable dynamical systems by domain decomposition Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, pp. 339-342, Vol.1048, 2008 Susanna Kube, Marcus Weber BibTeX

Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics Journal of Computational Physics, 228(6), pp. 1947-1962, 2008 (preprint available as ZIB-Report 07-17) Susanna Kube, Caroline Lasser, Marcus Weber PDF (ZIB-Report)
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Preserving the Markov Property of Reduced Reversible Markov Chains Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, pp. 593-596, Vol.1048, 2008 Susanna Kube, Marcus Weber BibTeX

Selection and flexible optimization of binding modes from conformation ensembles Biosystems, 92(1), pp. 42-48, 2008 A. Guerler, Sebastian Moll, Marcus Weber, Holger Meyer, Frank Cordes BibTeX
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2007

A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations Journal of Chemical Physics, 126(2), 2007 Susanna Kube, Marcus Weber BibTeX
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Conformation-based transition state theory ZIB-Report 07-18 Marcus Weber PDF
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Selection and flexible optimization of binding modes from conformation ensembles Biosystems, 2007 A. Gürler, Sebastian Moll, Marcus Weber, Holger Meyer, Frank Cordes BibTeX

Stable Computation of Probability Densities of Metastable Dynamical Systems SIAM J. Multiscale Model. Simul., 6(2), pp. 396-416, 2007 Marcus Weber, Susanna Kube, Lionel Walter, Peter Deuflhard BibTeX

Visualization of the tRNA(Ser) acceptor step binding site in the seryl-tRNA synthetase BBRC, 362(2), pp. 415-418, 2007 C. Förster, Arnd B. E. Brauer, J. Fürste, C. Betzel, Marcus Weber, Frank Cordes, V. Erdmann BibTeX

Vom Dietrich zum Sicherheitsschlüssel – Mathematiker des Matheon simulieren neuen Wirkstoff für die Diabetes-Behandlung DFG-Forschungszentrum Matheon, 2007 R. Kellermann, Marcus Weber, Alexander Bujotzek BibTeX

2006

An Indicator for the Number of Clusters From Data and Information Analysis to Knowledge Engineering, Myra Spiliopoulou, Rudolf Kruse, Christian Borgelt, Andreas Nürnberger, Wolfgang Gaul (Eds.), Springer Berlin Heidelberg, pp. 103-110, 2006 Marcus Weber, Wasinee Rungsarityotin, Alexander Schliep BibTeX

Coarse Grained Molecular Kinetics ZIB-Report 06-35 (Appeared as : "A coarse grained method for the identification of transition rates between molecular conformations" in Journal of Chemical Physics, 126(2) 2007) Susanna Kube, Marcus Weber PDF
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ConFlow? A new space-based Application for complete Conformational Analysis of Molecules ZIB-Report 06-31 Holger Meyer, Sebastian Moll, Frank Cordes, Marcus Weber PDF
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ConfJump : a fast biomolecular sampling method which drills tunnels through high mountains ZIB-Report 06-26 Lionel Walter, Marcus Weber PDF
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Efficient Sampling of the Stationary Distribution of Metastable Dynamical Systems ZIB-Report 07-03 Marcus Weber, Susanna Kube, Alexander Riemer, Alexander Bujotzek PDF
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Meshless Methods in Confirmation Dynamics Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, M. Dellnitz (Advisors), 2006 Marcus Weber PDF
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Meshless Methods in Conformation Dynamics Doctoral thesis, Freie Universität Berlin, department of mathematics, 2006 Marcus Weber BibTeX

Stable computation of probability densities for metastable dynamical systems ZIB-Report 06-39 (Appeared in: SIAM J. Multisc. Mod. Sim. 2007, 6(2), pp. 396-416) Marcus Weber, Lionel Walter, Susanna Kube, Peter Deuflhard PDF
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2005

Conformation Kinetics as a Reduced Model for Transition Pathways ZIB-Report 05-43 Susanna Kube, Marcus Weber PDF
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Identification of Metastabilities in Monomolecular Conformation Kinetics ZIB-Report 06-01 Susanna Kube, Marcus Weber PDF
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Robust Perron Cluster Analysis for Various Applications in Computational Life Science Computational Life Sciences, pp. 57-66, 2005 Marcus Weber, Susanna Kube BibTeX

Robust Perron Cluster Analysis in Conformation Dynamics Lin. Alg. Appl. – Special Issue on Matrices and Mathematical Biology, Elsevier Journals: Germany, pp. 161-184, 2005 (preprint available as ZIB-Report 03-19) Peter Deuflhard, Marcus Weber PDF (ZIB-Report)
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ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights ZIB-Report 05-17 Marcus Weber, Holger Meyer PDF
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2004

Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data ZIB-Report 04-39 Marcus Weber, Wasinee Rungsarityotin, Alexander Schliep PDF
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2003

Clustering by using a simplex structure ZIB-Report 04-03 Marcus Weber PDF
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Improved Perron Cluster Analysis ZIB-Report 03-04 Marcus Weber PDF
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2002

Characterization of Transition States in Conformational Dynamics using Fuzzy Sets ZIB-Report 02-12 Marcus Weber, Tobias Galliat PDF
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Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals ZIB-Report 02-40 Frank Cordes, Marcus Weber, Johannes Schmidt-Ehrenberg PDF
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