2024:

  1. A. Sikorski, A. Niknejad, M. Weber, L. Donati: Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies, J. Chem. Phys., 160:104112, 2024.
  2. A. Sikorski, E. Ribera Borrell, M. Weber: Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN, J. Math. Phys., 65:013502, 2024.
  3. L. Donati, K. Fackeldey, M. Weber: Augmented ant colony algorithm for virtual drug discovery, J. Math. Chem., 62:367-385, 2024.

2023:

  1. S. Chewle, M. Weber, F. Emmerling: 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):6737-6746, 2023.
  2. T. Boege, R. Fritze, C. Görgen, J. Hanselmann, D. Iglezakis, L. Kastner, T. Koprucki, T. Krause, C. Lehrenfeld, S. Polla, M. Reidelbach, C. Riedel, J. Saak, B. Schembera, K. Tabelow, M. Weber: Research-Data Management Planning in the German Mathematical Community, Eur. Math. Soc. Mag., epub ahead of print, 2023.
  3. C. Secker, K. Fackeldey, M. Weber, S. Ray, C. Gorgulla, C. Schütte: Novel multi-objective affinity approach allows to identify pH-specific mu-opioid receptor agonists, J. Cheminformatics, 15, 2023.
  4. L. Donati, M. Weber: Efficient Estimation of Transition Rates as Functions of pH, Proc. Appl. Math & Mechanics, epub ahead of print, 2023.
  5. T. Ternes, K.H. Bauer, F. Brauer, J. Drewes, A. Joss, G. Hiller, K. Jewell, J. Oehlmann, M. Radke, U. Schulte-Oehlmann, T. Schwartz, P. Seel, J. Völker, L. Weber, M. Weber: Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen, DWA-Themen, T1/2023, 2023.
  6. S. Ray, K. Fackeldey, C. Stein, M. Weber: Coarse-Grained MD Simulations of Opioid Interactions with the μ-Opioid Receptor and the Surrounding Lipid Membrane, Biophysica, 3(2):263-275, 2023.
  7. A. Thies, V. Sunkara, S. Ray, M. Ö. Celik, F. Yergöz, C. Schütte, C. Stein, M. Weber, S. Winkelmann: Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design, Scientific Reports, 13(607), 2023.

2022:

  1. R. Sechi, K. Fackeldey, S. Chewle, M. Weber: SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data, Algorithms, 15(9):297, 2022.
  2. P. Benner, M. Burger, D. Göddeke, C. Görgen, C. Himpe, J. Heiland, T. Koprucki, M. Ohlberger, S. Rave, M. Reidelbach, J. Saak, A. Schöbel, K. Tabelow, M. Weber: Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative), GAMM Rundbrief, 40-43, 2022.
  3. L. Donati, M. Weber: Assessing transition rates as functions of environmental variables, The Journal of Chemical Physics, 157(22):224103 (1-14), 2022.
  4. L. Donati, M. Weber, B. G. Keller: A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models, Journal of Mathematical Physics, 63:123306, 2022.
  5. R. Fernandes, S. Chowdhary, N. Mikula, N. Saleh, K. Kanevche, H. von Berlepsch, N. Hosogi, J. Heberle, M. Weber, C. Böttcher, B. Koksch: Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures, Angewandte Chemie, 61(48):e202208647, 2022. LINK
  6. F. Erlekam, M. Zumbansen, M. Weber: Parameter estimation on multivalent ITC data sets. Scientific Reports, 12:13402, 2022. LINK

2021:

  1. R. Sechi, M. Weber, K. Heyne: MSM building and projection for the analysis of time-resolved spectra, PAMM, 21(1):e202100102, 2021. LINK
  2. W. Bauer, M. Weber, E. Diehl-Wiesenecker, N. Galtung, M. Prpic, R. Somasundaram, R. Tauber, J. M. Schwenk, P. Micke, K. Kappert: Plasma proteome fingerprints reveal distinctiveness and clinical outcome of SARS-CoV-2 infection, Viruses, 13(12):2456, 2021. LINK
  3. S. Roehl, M. Weber, K.Fackeldey: Computing the minimal rebinding effect for nonreversible processes. SIAM MMS, 19(1):460-477, 2021.
  4. R. Sechi, A. Sikorski, M. Weber: Estimation of the Koopman generator by Newton's Extrapolation. SIAM MMS, 19(2):758–774, 2021.
  5. A. Sikorski, M. Weber, C. Schütte: The Augmented Jump Chain - a sparse representation of time-dependent Markov jump processes. Advanced Theory and Simulations, 4(4):2000274, 2021. LINK
  6. K. Fackeldey, J. Röhm, A. Niknejad, S. Chewle, M. Weber: Analyzing Raman Spectral Data without Separabiliy Assumption. J Math Chem, 59:575–596, 2021. LINK

2020:

  1. L. Donati, M. Weber, B. G. Keller: Markov models from the Square Root Approximation of the Fokker-Planck equation: calculating the grid-dependent flux. Journal of Physics: Condensed Matter, https://doi.org/10.1088/1361-648X/abd5f7 , 2020.
  2. S. Chewle, F. Emmerling, M. Weber: Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study. Crystals, 10(12):1107, 2020. LINK
  3. S. Ray, V. Sunkara, C. Schütte, M. Weber: How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs. Molecular Simulation, 46(18):1443-1452, 2020. DOI 10.1080/08927022.2020.1839660. LINK
  4. R. J. Rabben, S. Ray, M. Weber: ISOKANN: Invariant subspaces of Koopman Operators learned by a Neural Network. The J. of Chem. Phys., 153(11):114109, 2020. LINK
  5. Confidential list of authors: DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen — Festlegung von Parametern und Formaten. Beuth Verlag GmbH, 09/2020. LINK
  6. J. Villatoro, M. Zühlke, D. Riebe, T. Beitz, M. Weber, H.-G. Löhmannsröben: Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities. Analytical and Bioanalytical Chemistry, 412:5247-5260, 2020. LINK

2019:

  1. G. Del Vecchio, D. Labuz, J. Temp, V. Seitz, M. Kloner, R. Negrete, A. Rodriguez-Gaztelumendi, M. Weber, H. Machelska, C. Stein: pKa of opioid ligands as a discriminating factor for side effects. Scientific Reports, 9:19344, 2019. LINK
  2. F. Erlekam, S. Igde, S. Röblitz, L. Hartmann, M. Weber: Modelling of Multivalent Ligand-Receptor Binding Measured by kinITC. Computation, 7(3):46, 2019. LINK
  3. M. Weber: Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung. KA Korrespondenz Abwasser, Abfall, 7/2019:551-557, 2019.
  4. N. L. Venkatareddy, P. Wilke, N. Ernst, J. Horsch, A. Dallmann, M. Weber, H. G. Börner: 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):1900501, 2019. LINK
  5. N. Ernst, K. Fackeldey, A. Volkamer, O. Opitz, M. Weber: Computation of temperature-dependent dissociation rates of metastable protein-ligand complexes. Molecular Simulation, 45(11):904-911, 2019. LINK
  6. B. Reuter, K. Fackeldey, M. Weber: Generalized Markov modeling of nonreversible molecular kinetics. J. Chem. Phys., 150:174103, 2019. LINK
  7. K. Fackeldey, P. Koltai, P. Nevir, H. Rust, A.Schild, M. Weber: From Metastable to Coherent Sets -- time-discretization schemes. Chaos, 29:012101, 2019. LINK
  8. A. Abbas, I. Schneider, A. Bollmann, J. Funke, Jörg Oehlmann, C. Prasse, U. Schulte-Oehlmann, W. Seitz, T. Ternes, M. Weber, H. Wesely, M. Wagner: What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays. Water Research, 152:47-60, 2019. LINK
  9. J. Villatoro, M. Weber, M. Zühlke, A. Lehmann, K. Zenichowski, D. Riebe, T. Beitz, H.G. Löhmannsröben, O. Kreuzer: Structural characterization of synthetic peptides using electrospray ion mobility spectrometry and molecular dynamics simulations. International Journal of Mass Spectrometry, 436:108-117, 2019. LINK

2018:

  1. M. Reidelbach, M. Weber, P. Imhof: Prediction of perturbed proton transfer networks. PLoS ONE, 13(12): e0207718, 2018. LINK
  2. L. Donati, M. Heida, B. G. Keller, M. Weber: Estimation of the infinitesimal generator by square-root approximation. J. Phys.: Condens. Matter, 30(42):425201, 2018. LINK
  3. K. Fackeldey, A. Sikorski, M. Weber: Spectral Clustering for Non-Reversible Markov Chains. Comp. Appl. Math., 37:6376-6391, 2018. LINK
  4. S. Wagner, C. Zapata, W. Wan, K. Gawlitza, M. Weber, K. Rurack: Role of counterions in molecularly imprinted polymers for anionic species. Langmuir, 34(23):6963–6975, 2018. LINK
  5. B. Reuter, M. Weber, K. Fackeldey, S. Röblitz, M. Garcia: A generalized Markov State Modeling method for non-equilibrium biomolecular dynamics – exemplified on peptide conformational dynamics driven by an oscillating electric field. J. Chem. Theory Comput., 14(7):3579–3594, 2018. LINK
  6. V. Spahn, G. Del Vecchio, A. Rodriguez-Gaztelumendi, J. Temp, D. Labuz, M. Kloner, M. Reidelbach, H. Machelska, M. Weber, C. Stein: Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist. Scientific Reports, 8, Art. no. 8965, 2018. LINK
  7. J. Quer, L. Donati, B. G. Keller, M. Weber: An Automatic Adaptive Importance Sampling Algorithm for Molecular Dynamics in Reaction Coordinates. SIAM J. Sci. Comput., 40(2):A653-A670, 2018. LINK
  8. N. Djurdjevac Conrad, D. Fürstenauf, A. Grabundzija, L. Helfmann, M. Park, W. Schier, B. Schütt, C. Schütte, M. Weber, N. Wulkow, J. Zonker: Mathematical Modeling of the Spreading of Innovations in the Ancient World. eTopoi, 7:1-32, 2018. LINK
  9. I. Beckenbach, L. Eifler, K. Fackeldey, A. Gleixner, A. Grever, M. Weber, J. Witzig: Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes. Multiscale Model. Simul., 16(1):248-265, 2018. LINK
  10. M. Weber: Implications of PCCA+ in Molecular Simulation. Computation, 6(1):20, 2018. LINK
  11. K. Schrade, J. Tröger, A. Eldahshan, K. Zühlke, K. R. Abdul Azeez, J.M. Elkins, M. Neuenschwander, A. Oder, M. Elkewedi, S. Jaksch, K. Andrae, J. Li, J. Fernandes, P.M. Müller, S. Grunwald, S.F. Marino, T. Vukicevic, J. Eichhorst, B. Wiesner, M. Weber, M. Kapiloff, O. Rocks, O. Daumke, T. Wieland, S. Knapp, J.P. von Kries, E. Klussmann: 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):e0191423, 2018. LINK
  12. C. Hartmann, Ch. Schütte, M. Weber, W. Zhang: Importance sampling in path space for diffusion processes with slow-fast variables. Probab. Theory Relat. Fields, 170:177-228, 2018. LINK

2017:

  1. S. Igde, S. Röblitz, A. Müller, K. Kolbe, S. Boden, C. Fessele, Th. K. Lindhorst, M. Weber, L. Hartmann: Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH, Marcomolecular Bioscience, 17(12):1700198, 2017. LINK
  2. K. Fackeldey, A. Niknejad, M. Weber: Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation. Spec. Matrices, 5:73–81, 2017. LINK
  3. M. Weber, K. Fackeldey, C. Schütte: Set-free Markov State Model Building. The Journal of Chemical Physics,146(12):124133, 2017. LINK
  4. V. Spahn, G. Del Vecchio, D. Labuz, A. Rodriguez-Gaztelumendi, N. Massaly, J. Temp, V. Durmaz, P. Sabri, M. Reidelbach, H. Machelska, M. Weber, C. Stein: A nontoxic pain killer designed by modeling of pathological receptor conformations. Science, 355(6328):966-969, March 2017. LINK
  5. T. Ternes et al.: Anthropogene Spurenstoffe, Krankheitserreger und Antibiotikaresistenzen im Wasserkreislauf -- Relevanz, Monitoring und Eliminierung. DWA-Themen, Januar 2017.
  6. K. Fackeldey, M. Weber: GenPCCA -- Markov State Models for Non-Equilibrium Steady States. WIAS Report, 29:70-80, 2017. LINK

2016:

  1. L. von Krbek, A. Achazi, M. Solleder, M. Weber, B. Paulus, C. Schalley:Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements. Chem. Eur. J., 22(43):15475-15484, 2016.
  2. N. Djurdjevac Conrad, M. Weber, Ch. Schütte: Finding dominant structures of nonreversible Markov processes. A SIAM Interdisciplinary Journal, 14(4):1319-1340, 2016.
  3. J. Villatoro, M. Zühlke, D. Riebe, T. Beitz, M. Weber, J. Riedel, H-G. Löhmannsröben: IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector. International Journal for Ion Mobility Spectrometry, 19(4):197-207, 2016.

2015:

  1. A. Nielsen, M. Weber: Computing the nearest reversible Markov chain. Numerical Linear Algebra with Applications, 22(3):483-499, 2015.
  2. F. Abendroth, M. Solleder, D. Mangoldt, P. Welker, K. Licha, M. Weber, O. Seitz: High affinity fluorescence labelled ligands for the estrogen receptor. Eur. J. Org. Chem., 2015(10):2157-2166, 2015.
  3. S. Igde, H. Wöhlk, S. Röblitz, M. Reidelbach, M. Weber, L. Hartmann: Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC. Conference: Münster Symposium on Cooperative Effects 2015 - SFB 858, At Westfählische Wilhelms-Universität Münster, 2015.
  4. K. Koschek, V. Durmaz, O. Krylova, M. Wieczorek, S. Gupta, M. Richter, A. Bujotzek, C. Fischer, R. Haag, C. Freund, M. Weber, J. Rademann: 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, 11:837–847, 2015. .
  5. V. Durmaz, M. Weber, J. Meyer, H. Mückter: Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe in der Wassermatrix. KA Korrespondenz Abwasser, Abfall, 3/15:264-267, 2015.
  6. Ch. Schütte, A. Nielsen, M. Weber: Markov State Models and Molecular Alchemy. Molecular Physics, 113(1):69-78, 2015. Link

2014:

  1. M. Weber, C. Zoschke, A. Sedighi, E. Fleige, R. Haag, M. Schäfer-Korting: Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters. J Nanomed Nanotechnol, 5(5):234, 2014. doi: 10.4172/2157-7439.1000234 Link
  2. W. Zhang, H. Wan, C. Hartmann, M. Weber, C. Schütte: Applications of the cross-entropy method to importance sampling and optimal control of diffusions. SIAM Journal on Scientific Computing, 36(6):A2633-A2653, 2014.
  3. T. Ternes et al. (Arbeitsgruppe "Anthropogene Spurenstoffe im Wasserkreislauf" - Fachgruppe in der GDCh und DWA-Arbeitsgruppe): Bedeutung von Transformationsprodukten für den Wasserkreislauf. Link. DWA-Themen, KA 8.1, T 4/2014, August 2014.
  4. K. Andrae, S. Merkel, V. Durmaz, K. Fackeldey, R. Köppen, M. Weber, M. Koch: Investigation of the Ergopeptide Epimerization Process. Computation 2(3):102-111, 2014. Link
  5. M. Weber: Rechnergestützte (in silico-)Toxikologie, In: H. H. Dieter, I. Chorus, W. Krüger, B. Mendel (eds.), Trinkwasser aktuell. Erich Schmidt Verlag, ISBN 978-3-503-14103-6, chapter 1004.3 (1-15), 2014.
  6. C. Schütte, P. Deuflhard, F. Noé, M. Weber: A3 -- Design of functional molecules. EMS Series in Industrial and Applied Mathematics 1, Matheon -- Mathematics for Key Technologies, pp. 49-65, 2014.
  7. M. Weber, P. Deuflhard: SHOWCASE 1 -- Mathematics without pain. EMS Series in Industrial and Applied Mathematics 1, Matheon -- Mathematics for Key Technologies, pp. 26-27, 2014.
  8. K. Fackeldey, M. Weber: Local Refinements in Classical Molecular Dynamics Simulations. 2nd International Conference on Mathematical Modeling in Physical Sciences 2013, Journal of Physics: Conference Series, 490:012016, 2014. Link
  9. O. Scharkoi, S. Esslinger, R. Becker, M. Weber, I. Nehls: Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane. Molecular Simulation, online publication, DOI 10.1080/08927022.2014.898845, 2014.
  10. M. Weber, K. Fackeldey: Computing the Minimal Rebinding Effect Included in a Given Kinetics. Multiscale Model. Simul., 12(1):318-334, 2014. Link
  11. A. Bujotzek, O. Schütt, A. Nielsen, K. Fackeldey, M. Weber: ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling. Journal of Mathematical Chemistry, 52:781–804, 2014.

2013:

  1. F. Haack, K. Fackeldey, S. Röblitz, O. Scharkoi, M. Weber, B. Schmidt: Adaptive spectral clustering with application to tripeptide conformation analysis. J. Chem. Phys., 139:194110, 2013.
  2. V. Durmaz, S. Schmidt, P. Sabri, C. Piechotta, M. Weber: A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens. J. Chem. Inf. Model, 53(10):2681–2688, 2013. Link
  3. K. Andrae, V. Durmaz, K. Fackeldey, O. Scharkoi, M. Weber: Medizin aus dem Computer. Der Anaesthesist July 2013, Springer-Verlag Berlin Heidelberg, 2013. Link
  4. R. Tyagi, S. Malhotra, A. Thünemann, A. Sedighi, M. Weber, A. Schäfer, R. Haag: Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles. J. Phys. Chem. C, 117(23):12307–12317, 2013.
  5. H. C. Lie, K. Fackeldey, M. Weber: A Square Root Approximation of Transition Rates for a Markov State Model. SIAM. J. Matrix Anal. & Appl., 34(2):738–756, 2013. Link
  6. S. Röblitz, M. Weber: Fuzzy Spectral Clustering by PCCA+: Application to Markov State Models and Data Classification. Advances in Data Analysis and Clasification, 7(2):147-179, Link, 2013.
  7. O. Scharkoi, K. Fackeldey, I. Merkulow, K. Andrae, I. Nehls, D. Siegel, M. Weber: Conformational Analysis of Alternariol on the Quantum Level. J. Mol. Mod., 19(6):2567-2572, 2013.
  8. M. Shan, K. E. Carlson, A. Bujotzek, A. Wellner, R. Gust, M. Weber, J. A. Katzenellenbogen, R. Haag: Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor. ACS Chem. Biol., Link, 8(4):707-715, 2013.
  9. M. Weber: 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. 147-154, 2013.
  10. K. Fackeldey, A. Bujotzek, M. Weber: A meshless discretization method for Markov State Models applied to explicit water peptide folding simulations. In: Lecture Notes in Computational Science and Engineering, Vol 89, Meshfree Methods for Partial Differential Equations VI, M. Griebel, M.A. Schweitzer (Eds.), Springer, pp. 141-154, 2013.

2012:

  1. 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., 60(47):11733–11740, 2012.
  2. 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., 51(42):10472–10498, 2012.
  3. M. Weber, A. Bujotzek, R. Haag: Quantifying the rebinding effect in multivalent chemical ligand-receptor systems. Journal of Chemical Physics, 137(5):054111, 2012.
  4. K. Fackeldey, M. Klimm, M. Weber: A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules. Journal of Mathematical Chemistry , 50(9):2623-2635, 2012.
  5. V. Durmaz, M. Weber, R. Becker: How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: Application in the Liquid Chromatographic Separation of Hexabromocyclododecane Stereoisomers. Journal of Molecular Modeling, 18(6):2399-2408, 2012.

2011:

  1. O. Scharkoi, S. Esslinger, R. Becker, M. Weber, I. Nehls: Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites. Organohalogen Compounds, 73:730-733, 2011.Link
  2. K. Fackeldey, S. Röblitz, O. Scharkoi, M. Weber: 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.), 899-909, 2011.
  3. M. Shan, A. Bujotzek, F. Abendroth, O. Seitz, M. Weber, R. Haag: Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding. ChemBioChem, 12(17):2587-2598, 2011.
  4. F. Abendroth, A. Bujotzek, M. Shan, R. Haag, M. Weber, O. Seitz: DNA-controlled bivalent presentation of ligands for the estrogen receptor. Angewandte Chemie Int. Ed., 50(37):8592-8596, 2011.
  5. 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. Molecular Simulation, 37(11):899-906, 2011.
  6. V. Durmaz, K. Fackeldey, M. Weber: A rapidly-mixing Monte Carlo method for the simulation of slow molecular processes. In: Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science, C. J. Mode (ed.), ISBN: 978-953-307-427-6, InTech, chapter 22, 2011.
  7. A. Bujotzek, M. Shan, R. Haag, M. Weber: Towards a rational spacer design for bivalent inhibition of estrogen receptor. JCAMD Journal of Computer-Aided Molecular Design, 25(3):253–262, 2011.
  8. Ch. Scheibe, A. Bujotzek, J. Dernedde, M. Weber, O. Seitz: DNA-programmed spatial screening of carbohydrate-lectin interactions. Chemical Science, 2:770-775, 2011.
  9. M. Klimm, A. Bujotzek, M. Weber: Direct Reweighting Strategies in Conformation Dynamics. MATCH Communications in Mathematical and in Computer Chemistry, 65(2):333-346, 2011.

2010:

  1. F. Haack, S. Röblitz, O. Scharkoi, B. Schmidt, M. Weber: Adaptive Spectral Clustering for Conformation Analysis. ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics, AIP Conf. Proc., 1281:1585-1588, 2010.
  2. H. H. Dieter, K. Götz, K. Kümmerer, B. Rechenberg, F. Keil: Handlungsmöglichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren Rückständen in das Roh- und Trinkwasser. Link. Contributions to the manuscript
  3. Ph. Metzner, M. Weber, Ch. Schütte: Observation uncertainty in reversible Markov chains. Phys. Rev. E, 82(3):031114, 2010.
  4. 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, 1217:2206-2215, March 2010.
  5. M. Weber, K. Andrae: A simple method for the estimation of entropy differences. MATCH Communications in Mathematical and in Computer Chemistry, 63(2):319-332, 2010.

2009:

  1. M. Weber, V. Durmaz, R. Becker, S. Esslinger: Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR. Organohalogen Compounds, 71:247-252, 2009. Link
  2. M. Weber: Spurenstoffe im Trinkwasser - Risikoqualifizierung im Rechner? In: Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene e.V., Band 134 (CD-ROM), L. Dunemann and O. Schmoll (eds.), November 2009.
  3. S. Röblitz, M. Weber: Fuzzy Spectral Clustering by PCCA+. In: Classifcation and Clustering: Models, Software and Applications, H.J. Mucha and G. Ritter (eds.), WIAS Report 26:73-79, September 2009.
  4. A. Bujotzek, M. Weber: Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach. Journal of Bioinformatics and Computational Biology, 7(5):811-831, April 2009.

2008:

  1. R. Köppen, R. Becker, M. Weber, V. Durmaz, I. Nehls: HBCD stereoisomers: Thermal interconversion and enantiospecific trace analysis in biota. Organohalogen Compounds, 70:910-913, 2008.
  2. S. Kube, C. Lasser, M. Weber: Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. Journal of Computational Physics, J. Comp. Phys., 228(6):1947-1962, November 2008.
  3. S. Kube, M. Weber: Computation of equillibrium densities in metastable dynamical systems by domain decomposition. Numerical Analysis and Applied Mathematics, Int. Conf. on Num. Analy. and Appl. Math. 2008, AIP Conference Proceedings, Kos, 1048:339-342, September 2008.
  4. M. Weber, S. Kube: Preserving the Markov Property of Reduced Reversible Markov Chains. Numerical Analysis and Applied Mathematics, Int. Conf. on Num. Analy. and Appl. Math. 2008, AIP Conference Proceedings, Kos, 1048:593-596, September 2008.
  5. M. Weber, R. Becker, R. Köppen, V. Durmaz: Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers. Molecular Simulation, 34(7):727 - 736, June 2008.
  6. A. Guerler, S. Moll, M. Weber, H. Meyer, F. Cordes: Selection and flexible optimization of binding modes from conformation ensembles. Biosystems, URL 92(1):42-48, April 2008.

2007:

  1. C. Förster, A.B.E. Brauer, J.P. Fürste, C. Betzel, M. Weber, F. Cordes, V.A. Erdmann: Superposition of a tRNA(Ser) acceptor stem microhelix into the seryl-tRNA synthetase complex, BBRC 2007, 362:415-418.
  2. M. Weber, S. Kube, L. Walter, P. Deuflhard: Stable Computation of Probability Densities for Metastable Dynamical Systems, SIAM J. Multisc. Mod. Sim. 2007, 6(2).
  3. S. Kube, M. Weber: A Coarse-Graining Method for the Identification of Transition Rates between Molecular Conformations, J. Chem. Phys. 2007, 126(2).

2006:

  1. M. Weber, W. Rungsarityotin, A. Schliep: An Indicator for the Number of Clusters Using a Linear Map to Simplex Structure, in: From Data and Information Analysis to Knowledge Engineering, 29th Annual Conference of the German Classification Society 2005, March 9-11, Studies in Classification, Data Analysis, and Knowledge, Springer, Heidelberg 2006, 103-110.

2005:

  1. M. Weber, S. Kube: Robust Perron Cluster Analysis for Various Applications in Computational Life Science, in: Computational Life Sciences: First International Symposium, CompLife 2005, September 25-27, (Ed. M.R. Berthold et al.) Springer, Heidelberg 2005, 57-66.
  2. P. Deuflhard, M. Weber: Robust Perron Cluster Analysis in Conformation Dynamics, Lin. Alg. App. 2005, 398c, Special issue on matrices and mathematical biology, 161-184.