Dr. Marcus Weber - Mitarbeiter
Zuse-Institut Berlin (ZIB)
Bereich Numerische Mathematik
Abteilung Numerische Analysis und Modellierung
Takustr. 7
D-14195 Berlin-Dahlem
Germany
Email: weber
zib.de
Telefon: +49 30 84185-189
Fax: +49 30 84185-107
Raum: 4106
Bereich Numerische Mathematik
Abteilung Numerische Analysis und Modellierung
Takustr. 7
D-14195 Berlin-Dahlem
Germany
Email: weber
zib.deTelefon: +49 30 84185-189
Fax: +49 30 84185-107
Raum: 4106
URL: Personal Homepage
Publikationen
2013 |
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| Marcus Weber, Konstantin Fackeldey | Computing the Minimal Rebinding Effect Included in a Given Kinetics | ZIB-Report 13-12 | PDF BibTex | RIS |
2012 |
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| K. Fackeldey, M. Klimm, M. Weber | A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules | J. Math. Chem., Vol. 5, No. 9, pp. 2623 - 2635, 2012 | BibTex | RIS |
| K. Fackeldey, A. Bujotzek, M. Weber | A meshless discretization method for Markov state models applied to explicit water peptide folding simulations | Meshfree Methods for Partial Differential Equations VI, Lecture Notes in Computational Science and Engineering, Vol. 89, pp. 141-154, Springer, 2012 | BibTex | RIS |
| Burcu Tunga, Marcus Weber | Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration | ZIB-Report 12-35 | PDF BibTex | RIS |
| V. Durmaz, R. Becker, M. Weber | How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: Application in the Liquid Chromatographic Separation of Hexabromocyclododecane Stereoisomers | J. Mol. Model., Vol. 18, pp. 2399-2408, 2012 | BibTex | RIS |
| C. Fasting, C.A. Schalley, M. Weber, O. Seitz, S. Hecht, B. Koksch, J. Dernedde, C. Graf, E.-W. Knapp, R. Haag | Multivalency as a Chemical Organization and Action Principle | Angew. Chem. Int. Ed., Vol. 51, No. 42, pp. 10472 - 10498, 2012 | BibTex | RIS |
| R. Köppen, J. Riedel, M. Proske, S. Drzymala, T. Rasenko, V. Durmaz, M. Weber, M. Koch | Photochemical trans-/cis-isomerization and quantification of zearalenone in edible oils | J. Agric. Food Chem., Vol. 60, pp. 11733-11740, 2012 | BibTex | RIS |
| M. Weber, A. Bujotzek, R. Haag | Quantifying the rebinding effect in multivalent chemical ligand-receptor systems | J. Chem. Phys., Vol. 137, No. 5, pp. 054111, 2012 | BibTex | RIS |
| Marcus Weber | The funnel trap paradox | ZIB-Report 12-12 | PDF BibTex | RIS |
2011 |
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| Marcus Weber | A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator | Habilitation thesis, Freie Universität Berlin, 2011 | PDF BibTex | RIS |
| 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. J. Mode (Ed.), InTech, 2011 | BibTex | RIS |
| M. Weber, A. Bujotzek, K. Andrae, M. Weinhart, R. Haag | Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces | J. Mol. Sim., 2011 | BibTex | RIS |
| F. Abendroth, A. Bujotzek, M. Shan, R. Haag, M. Weber, O. Seitz | DNA-controlled bivalent presentation of ligands for the estrogen receptor | Angew. Chem. Int. Ed., 2011 | BibTex | RIS |
| Ch. Scheibe, A. Bujotzek, J. Dernedde, M. Weber, O. Seitz | DNA-programmed spatial screening of carbohydrate-lectin interactions | Chem. Sci., Vol. 2, pp. 770-775, 2011 | BibTex | RIS |
| M. Klimm, A. Bujotzek, M. Weber | Direct Reweighting Strategies in Conformation Dynamics | MATCH Commun. Math. Comp. Chem., Vol. 65(2), pp. 333-346, 2011 | BibTex | RIS |
| Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber | Soft Versus Hard Metastable Conformations in Molecular Simulations | ZIB-Report 11-27 | PDF BibTex | RIS |
| A. Bujotzek, M. Shan, R. Haag, M. Weber | Towards a rational spacer design for bivalent inhibition of estrogen receptor | J. Comput.-Aided Mol. Des., Vol. 25(3), pp. 253-262, 2011 | BibTex | RIS |
2010 |
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| M. Weber, K. Andrae | A simple method for the estimation of entropy differences | MATCH Commun. Math. Comp. Chem. 2010, Vol. 63(2), pp. 319-332, 2010 | BibTex | RIS |
| F. Haack, S. Röblitz, O. Scharkoi, B. Schmidt, M. Weber | Adaptive Spectral Clustering for Conformation Analysis | AIP Conference Proceedings, Vol. 1281, No. 1, pp. 1585-1588, AIP, 2010 | DOI BibTex | RIS |
| D. Siegel, K. Andrae, M. Proske, C. Kochan, M. Koch, M. Weber, I. Nehls | 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 | BibTex | RIS |
| Ph. Metzner, M. Weber, Ch. Schütte | Observation uncertainty in reversible Markov chains | Phys. Rev. E, Vol. 82, No. 3, pp. 031114, American Physical Society, 2010 | DOI BibTex | RIS |
2009 |
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| Marcus Weber | A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator | ZIB-Report 09-27 | PDF BibTex | RIS |
| A. Bujotzek, M. Weber | 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 | BibTex | RIS |
| R. Köppen, R. Becker, M. Weber, V. Durmaz, I. Nehls | HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota | Organohalogen Compounds, Vol. 70, pp. 910-913, 2009 | BibTex | RIS |
| M. Weber, V. Durmaz, R. Becker, S. Esslinger | Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR | Organohalogen Compounds, Vol. 71, pp. 247-252, 2009 | BibTex | RIS |
| M. Weber | Spurenstoffe im Trinkwasser - Risikoqualifizierung im Rechner? | Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, L. Dunemann, O. Schmoll (Eds.), 2009 | BibTex | RIS |
2008 |
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| Marcus Weber | An efficient analysis of rare events in canonical ensemble dynamics | ZIB-Report 08-36 | PDF BibTex | RIS |
| M. Weber, R. Becker, R. Köppen, V. Durmaz | Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane | Journal of Molecular Simulation, Vol. 34, No. 7, pp. 727-736, 2008 | PDF (Preprint) BibTex | RIS |
| S. Kube, M. Weber | 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, Vol. 1048, pp. 339-342, AIP Conference Proceedings, 2008 | BibTex | RIS |
| S. Kube, C. Lasser, M. Weber | Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics | J. Comp. Phys., Vol. 228, No. 6, pp. 1947-1962, 2008 | PDF (Preprint) BibTex | RIS |
| S. Kube, M. Weber | Preserving the Markov Property of Reduced Reversible Markov Chains | Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, Vol. 1048, pp. 593 - 596, 2008 | BibTex | RIS |
| A. Guerler, S. Moll, M. Weber, H. Meyer, F. Cordes | Selection and flexible optimization of binding modes from conformation ensembles | Biosystems, Vol. 92, No. 1, pp. 42-48, 2008 | DOI BibTex | RIS |
2007 |
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| S. Kube, M. Weber | A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations | J. Chem. Phys., Vol. 126, No. 2, 2007 | BibTex | RIS |
| Marcus Weber | Conformation-based transition state theory | ZIB-Report 07-18 | PDF BibTex | RIS |
| Marcus Weber, Susanna Kube, Alexander Riemer, Alexander Bujotzek | Efficient Sampling of the Stationary Distribution of Metastable Dynamical Systems | ZIB-Report 07-03 | PDF BibTex | RIS |
| M. Weber, S. Kube, L. Walter, P. Deuflhard | Stable Computation of Probability Densities of Metastable Dynamical Systems | SIAM J. Multiscale Model. Simul., Vol. 6, No. 2, pp. 396-416, 2007 | BibTex | RIS |
| C. Förster, A.B.E. Brauer, J.P. Fürste, C. Betzel, M. Weber, F. Cordes, V.A. Erdmann | Visualization of the tRNA(Ser) acceptor step binding site in the seryl-tRNA synthetase | BBRC, Vol. 362, No. 2, pp. 415-418, 2007 | BibTex | RIS |
| R. Kellermann, M. Weber, A. Bujotzek | Vom Dietrich zum Sicherheitsschlüssel -- Mathematiker des Matheon simulieren neuen Wirkstoff für die Diabetes-Behandlung | DFG-Forschungszentrum Matheon, 2007 | BibTex | RIS |
2006 |
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| M. Weber, W. Rungsarityotin, A. Schliep | An Indicator for the Number of Clusters: Using a Linear Map to Simplex Structure | From Data and Information Analysis to Knowledge Engineering, Myra Spiliopoulou, Rudolf Kruse, Christian Borgelt, Andreas Nürnberger, Wolfgang Gaul (Eds.), pp. 103-110, Springer Berlin Heidelberg, 2006 | DOI BibTex | RIS |
| Susanna Kube, Marcus Weber | Coarse Grained Molecular Kinetics | Appeared as : "A coarse grained method for the identification of transition rates between molecular conformations" in Journal of Chemical Physics, 126(2) 2007, | PDF (Preprint) BibTex | RIS |
| Holger Meyer, Sebastian Moll, Frank Cordes, Marcus Weber | ConFlow? A new space-based Application for complete Conformational Analysis of Molecules | ZIB-Report 06-31 | PDF BibTex | RIS |
| Lionel Walter, Marcus Weber | ConfJump : a fast biomolecular sampling method which drills tunnels through high mountains | ZIB-Report 06-26 | PDF BibTex | RIS |
| Susanna Kube, Marcus Weber | Identification of Metastabilities in Monomolecular Conformation Kinetics | ZIB-Report 06-01 | PDF BibTex | RIS |
| Marcus Weber | Meshless Methods in Confirmation Dynamics | Doctoral thesis, Freie Universität Berlin, 2006 | PDF BibTex | RIS |
| Marcus Weber, Lionel Walter, Susanna Kube, Peter Deuflhard | Stable computation of probability densities for metastable dynamical systems | Appeared in: SIAM J. Multisc. Mod. Sim. 2007, 6(2), pp. 396-416, | PDF (Preprint) BibTex | RIS |
2005 |
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| Susanna Kube, Marcus Weber | Conformation Kinetics as a Reduced Model for Transition Pathways | ZIB-Report 05-43 | PDF BibTex | RIS |
| M. Weber, S. Kube | Robust Perron Cluster Analysis for Various Applications in Computational Life Science | Computational Life Sciences: First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005, M. R. Berthold, et al. (Eds.), pp. 57-66, 2005 | BibTex | RIS |
| P. Deuflhard, M. Weber | Robust Perron Cluster Analysis in Conformation Dynamics | Lin. Alg. Appl. -- Special Issue on Matrices and Mathematical Biology, M. Dellnitz, S. Kirkland, M. Neumann, Ch. Schütte (Eds.), Vol. 398, pp. 161-184, Elsevier Journals: Germany, 2005 | PDF (Preprint) PDF (Preprint) BibTex | RIS |
| Marcus Weber, Holger Meyer | ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights | ZIB-Report 05-17 | PDF BibTex | RIS |
2004 |
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| Marcus Weber | Clustering by using a simplex structure | ZIB-Report 04-03 | PDF BibTex | RIS |
| Marcus Weber, Wasinee Rungsarityotin, Alexander Schliep | Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data | ZIB-Report 04-39 | PDF BibTex | RIS |
2003 |
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| Marcus Weber | Improved Perron Cluster Analysis | ZIB-Report 03-04 | PDF BibTex | RIS |
2002 |
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| Marcus Weber, Tobias Galliat | Characterization of Transition States in Conformational Dynamics using Fuzzy Sets | ZIB-Report 02-12 | PDF BibTex | RIS |
| Frank Cordes, Marcus Weber, Johannes Schmidt-Ehrenberg | Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals | ZIB-Report 02-40 | PDF BibTex | RIS |