@article{PoethkowWeberHege2011, author = {P{\"o}thkow, Kai and Weber, Britta and Hege, Hans-Christian}, title = {Probabilistic Marching Cubes}, volume = {30}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/j.1467-8659.2011.01942.x}, pages = {931 -- 940}, year = {2011}, language = {en} } @inproceedings{WeberMoellerVerbavatzetal.2011, author = {Weber, Britta and M{\"o}ller, Marit and Verbavatz, Jean-Marc and Baum, Daniel and Hege, Hans-Christian and Prohaska, Steffen}, title = {Fast Tracing of Microtubule Centerlines in Electron Tomograms}, booktitle = {BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization}, year = {2011}, language = {en} } @article{GoubergritsWeberPetzetal.2009, author = {Goubergrits, Leonid and Weber, Sarah and Petz, Christoph and Spuler, Andreas and P{\"o}thke, Jens and Berthe, Andr{\´e} and Hege, Hans-Christian}, title = {Wall-PIV as a Near Wall Flow Validation Tool for CFD}, volume = {12}, journal = {Journal of Visualization}, number = {3}, pages = {241 -- 250}, year = {2009}, language = {en} } @inproceedings{DercksenWeberGuentheretal.2009, author = {Dercksen, Vincent J. and Weber, Britta and G{\"u}nther, David and Oberlaender, Marcel and Prohaska, Steffen and Hege, Hans-Christian}, title = {Automatic alignment of stacks of filament data}, booktitle = {Proc. IEEE International Symposium on Biomedical Imaging}, publisher = {IEEE press}, address = {Boston, USA}, pages = {971 -- 974}, year = {2009}, language = {en} } @article{SahnerWeberLameckeretal.2008, author = {Sahner, Jan and Weber, Britta and Lamecker, Hans and Prohaska, Steffen}, title = {Extraction of feature Lines on surface meshes based on discrete Morse theory}, volume = {27}, journal = {Computer Graphics Forum}, number = {3}, address = {Eindhoven, Netherlands}, doi = {10.1111/j.1467-8659.2008.01202.x}, pages = {735 -- 742}, year = {2008}, language = {en} } @article{KoschekDurmazKrylovaetal.2015, author = {Koschek, and Durmaz, Vedat and Krylova, and Wieczorek, and Gupta, Pooja and Richter, and Bujotzek, Alexander and Fischer, and Haag, Rainer and Freund, and Weber, Marcus and Rademann,}, title = {Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands}, volume = {11}, journal = {Beilstein J. Org. Chem.}, pages = {837 -- 847}, year = {2015}, language = {en} } @article{DurmazWeberMeyeretal.2015, author = {Durmaz, Vedat and Weber, Marcus and Meyer, and M{\"u}ckter,}, title = {Computergest{\"u}tzte Simulationen zur Absch{\"a}tzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix}, volume = {3/15}, journal = {KA Korrespondenz Abwasser, Abfall}, pages = {264 -- 267}, year = {2015}, language = {de} } @misc{WeberFackeldey2015, author = {Weber, Marcus and Fackeldey, Konstantin}, title = {G-PCCA: Spectral Clustering for Non-reversible Markov Chains}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55505}, year = {2015}, abstract = {Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We extend this spectral clustering method also to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension, non-reversible Markov chains can be analyzed. Furthermore, the chains need not have a positive stationary distribution. And additionally to metastabilities, dominant cycles and sinks can be identified, too.}, language = {en} } @misc{DjurdjevacConradWeberSchuette2015, author = {Djurdjevac Conrad, Natasa and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Finding dominant structures of nonreversible Markov processes}, issn = {1438-0064}, doi = {10.1137/15M1032272}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55739}, year = {2015}, abstract = {Finding metastable sets as dominant structures of Markov processes has been shown to be especially useful in modeling interesting slow dynamics of various real world complex processes. Furthermore, coarse graining of such processes based on their dominant structures leads to better understanding and dimension reduction of observed systems. However, in many cases, e.g. for nonreversible Markov processes, dominant structures are often not formed by metastable sets but by important cycles or mixture of both. This paper aims at understanding and identifying these different types of dominant structures for reversible as well as nonreversible ergodic Markov processes. Our algorithmic approach generalizes spectral based methods for reversible process by using Schur decomposition techniques which can tackle also nonreversible cases. We illustrate the mathematical construction of our new approach by numerical experiments.}, language = {en} } @article{AbendrothSollederWelkeretal.2015, author = {Abendroth, Frank and Solleder, Marthe and Welker, Pia and Licha, Kai and Weber, Marcus and Seitz, Oliver and Mangoldt, Dorothea}, title = {High affinity flourescence labelled ligands for the estrogen receptor}, volume = {2015}, journal = {Eur. J. Org. Chem.}, number = {10}, pages = {2157 -- 2166}, year = {2015}, language = {en} } @article{WeberZoschkeSedighietal.2014, author = {Weber, Marcus and Zoschke, Christian and Sedighi, Amir and Fleige, Emanuel and Haag, Rainer and Sch{\"a}fer-Korting, Monika}, title = {Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters}, volume = {5}, journal = {J Nanomed Nanotechnol}, number = {5}, doi = {10.4172/2157-7439.1000234}, pages = {234}, year = {2014}, language = {en} } @misc{SteinWeberZoellneretal.2013, author = {Stein, Christoph and Weber, Marcus and Z{\"o}llner, Christian and Scharkoi, Olga}, title = {Fentanyl derivatives as pH-dependent opioid receptor agonists}, journal = {European Patent Application, Bulletin 2013/08}, year = {2013}, language = {en} } @misc{SteinWeberScharkoietal.2013, author = {Stein, Christoph and Weber, Marcus and Scharkoi, Olga and Deuflhard, Peter}, title = {Method and system for identifying compounds that bind and preferably activate a target opioid receptor in a pH-dependent manner}, journal = {European Patent Application, Bulletin 2013/28}, year = {2013}, language = {en} } @article{ZhangWangHartmannetal.2014, author = {Zhang, Wei and Wang, Han and Hartmann, Carsten and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Applications of the cross-entropy method to importance sampling and optimal control of diffusions}, volume = {36}, journal = {Siam Journal on Scientific Computing}, number = {6}, doi = {10.1137/14096493X}, pages = {A2654 -- A2672}, year = {2014}, language = {en} } @article{AndraeMerkelDurmazetal.2014, author = {Andrae, Karsten and Merkel, Stefan and Durmaz, Vedat and Fackeldey, Konstantin and K{\"o}ppen, Robert and Weber, Marcus and Koch, Matthias}, title = {Investigation of the Ergopeptide Epimerization Process}, volume = {2}, journal = {Computation}, number = {3}, doi = {10.3390/computation2030102}, pages = {102 -- 111}, year = {2014}, abstract = {Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that "folding" the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations.}, language = {en} } @misc{DeuflhardWeber2014, author = {Deuflhard, Peter and Weber, Marcus}, title = {Mathematics without pain}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, doi = {10.4171/137}, pages = {26 -- 28}, year = {2014}, language = {en} } @article{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0113222}, pages = {e113222}, year = {2014}, language = {en} } @misc{RedemannWeberMoelleretal.2014, author = {Redemann, Stefanie and Weber, Britta and M{\"o}ller, Marit and Verbavatz, Jean-Marc and Hyman, Anthony and Baum, Daniel and Prohaska, Steffen and M{\"u}ller-Reichert, Thomas}, title = {The Segmentation of Microtubules in Electron Tomograms Using Amira}, journal = {Mitosis: Methods and Protocols}, publisher = {Springer}, doi = {10.1007/978-1-4939-0329-0_12}, pages = {261 -- 278}, year = {2014}, language = {en} } @article{SchuetteNielsenWeber2015, author = {Sch{\"u}tte, Christof and Nielsen, Adam and Weber, Marcus}, title = {Markov State Models and Molecular Alchemy}, volume = {113}, journal = {Molecular Physics}, number = {1}, doi = {10.1080/00268976.2014.944597}, pages = {69 -- 78}, year = {2015}, abstract = {In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.}, language = {en} } @article{WeberFackeldey2014, author = {Weber, Marcus and Fackeldey, Konstantin}, title = {Computing the Minimal Rebinding Effect Included in a Given Kinetics}, volume = {12}, journal = {Multiscale Model. Simul.}, number = {1}, doi = {10.1137/13091124X}, pages = {318 -- 334}, year = {2014}, abstract = {The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory.}, language = {en} }