Publikationen
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 |
| 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, p. 054111, 2012 | BibTex | RIS |
2011 |
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| 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 |
| K. Fackeldey | Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach | IJPAM, Vol. 69, No. 2, pp. 185-202, 2011 | BibTex | RIS |
| K. Fackeldey, D. Krause, R. Krause, C. Lenzen | Coupling Molecular Dynamics and Continua with Weak Constraints | SIAM Multiscale Model. Simul., Vol. 9, pp. 1459 - 1494, 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 |
| 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 |
| C. Lasser, S. Röblitz | Computing expectation values for molecular quantum dynamics | SIAM J. Sci. Comput., Vol. 32, No. 3, pp. 1465-1483, 2010 | 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 |
| K. Fackeldey, D. Krause, R. Krause | Numerical Validation of Constraints Based Multiscale Methods | Proc. Meshfree Methods for Partial Differential Equations V, Lecture Notes in Computational Science and Engineering, M. Griebel, M. A. Schweitzer (Eds.), pp. 141-154, 2010 | BibTex | RIS |
| Ph. Metzner, M. Weber, Ch. Schütte | Observation uncertainty in reversible Markov chains | Phys. Rev. E, Vol. 82, No. 3, p. 031114, American Physical Society, 2010 | DOI BibTex | RIS |
2009 |
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| 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 |
| K. Fackeldey, R. Krause | Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics | Int. J. Numer. Meth. Engrg, Vol. 79, pp. 1517-1535, 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 |
| K. Fackeldey | The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics | Dissertation in Mathematics, Institute for Numerical Simulation, Uni Bonn 2009 | BibTex | RIS |
| V. Durmaz | Theoretical Investigations on HBCD and PBCD: Interconversion Rates and Receptor Binding Processes | Master Thesis, Freie Universität Berlin 2009 | BibTex | RIS |
| 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. 1023 pp, 2009 | BibTex | RIS |
2008 |
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| P. Deuflhard, W. Huisinga, T. Jahnke, M. Wulkow | Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation | SIAM J. Sci. Comput, Vol. 30, No. 6, pp. 2990-3011, 2008 | BibTex | RIS |
| K. Fackeldey, R. Krause | CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach | Proceedings GAMM 2008, Proc. Appl. Math. Mech., Vol. 8, No. 1, p. 10495 pp, 2008 | 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 | 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 |
| I. Reinecke, P. Deuflhard | Model Development and Decomposition in Physiology | Handbook of Research on Systems Biology Applications in Medicine, A. Daskalaki (Ed.), Vol. 2, pp. 759-797, 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 | 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 |
| K. Fackeldey, R. Krause | Quadrature and Implementation of the Weak Coupling Method | Proceedings of the fourth Int. Conf. Multiscale Materials Modeling 2008, Proc. Appl. Math. Mech., Anter El-Azab (Ed.), p. 1023 pp, 2008 | BibTex | RIS |
| K. Fackeldey, R. Krause, M.A. Schweitzer | Stability of Energy Transfer in the Weak Coupling Method | Meshfree Methods for Partial Differential Equations IV, Lecture Notes in Computational Science and Engineering, M. Griebel, M. A. Schweitzer (Eds.), Vol. 65, pp. 111-121, 2008 | 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 |
| I. Reinecke, P. Deuflhard | A Complex Mathematical Model of the Human Menstrual Cycle | Journal of Theoretical Biology, Vol. 247, No. 2, pp. 303-330, 2007 | BibTex | RIS |
| D. Baum | A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules | Dissertation, Freie Universität Berlin 2007 | BibTex | RIS |
| O. Scharkoi | Simulation von Opioiden unter Hinzunahme von Temperatur und pH-Wert | Bachelor Thesis, Freie Universität Berlin, Bioinformatik 2007 | BibTex | RIS |
| K. Fackeldey, R. Krause | Solving Frictional Contact Problems with Multigrid Efficiency | Proc.of the 16th International Conference on Domain Decomposition Methods, Lecture Notes in Computational Science and Engineering, Olof B.; Keyes David E. Widlund (Ed.), Vol. 50, pp. 547-554, 2007 | 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 |
| K. Andrae, P.-G. Reinhard, E. Suraud | Systematics of spin-polarized small Na clusters | 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 |
| K. Fackeldey, R. Krause | Weak coupling in function space: a unifying coupling approach for multiscale simulations | Proceedings ICIAM 2007, Proc. Appl. Math. Mech., Vol. 7, No. 1, p. 2020113 pp, 2007 | BibTex | RIS |
2006 |
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| Alexander Riemer | Accuracy, stability, convergence of rigorous thermodynamic sampling methods | Master's thesis, Freie Universität Berlin, department of bioinformatics 2006 | BibTex | RIS |
| 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 |
| Marcus Weber | Meshless Methods in Conformation Dynamics | Doctoral thesis, Freie Universität Berlin, department of mathematics 2006 | BibTex | RIS |
| K. Andrae, P.M. Dinh, P.-G. Reinhard, E. Suraud | Pump and probe analysis of metal cluster dynamics | Computational Materials Science, Vol. 35, No. 3, pp. 169 - 173, 2006 | DOI BibTex | RIS |
| A. Gürler | Selection and flexible optimization of binding modes from conformation ensembles. | Diploma thesis, Freie Universität Berlin, department of bioinformatics 2006 | BibTex | RIS |
2005 |
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| 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 | BibTex | RIS |
2004 |
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| K. Andrae, P.-G. Reinhard, E. Suraud | Crossed Beam Pump and Probe Dynamics in Metal Clusters | Phys. Rev. Lett., Vol. 92, No. 17, p. 173402, American Physical Society, 2004 | DOI BibTex | RIS |
2001 |
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| S. Kümmel, K. Andrae, P.-G. Reinhard | Collectivity in the optical response. of small metal clusters | Applied Physics B: Lasers and Optics, Vol. 73, pp. 293-297, Springer Berlin / Heidelberg, 2001 | DOI BibTex | RIS |
1998 |
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| A. Fischer, F. Cordes, Ch. Schütte | Hybrid Monte Carlo with Adaptive Temperature in Mixed--Canonical Ensemble: Efficient Conformational Analysis of RNA | J. Comp. Chem., Vol. 19, No. 15, pp. 1689-1697, 1998 | BibTex | RIS |