@article{HaackRoeblitzScharkoietal.2010, author = {Haack, Fiete and R{\"o}blitz, Susanna and Scharkoi, Olga and Schmidt, Burkhard and Weber, Marcus}, title = {Adaptive Spectral Clustering for Conformation Analysis}, volume = {1281}, journal = {AIP Conference Proceedings}, number = {1}, publisher = {AIP}, doi = {10.1063/1.3498116}, pages = {1585 -- 1588}, year = {2010}, language = {en} } @article{KubeWeber2007, author = {Kube, Susanna and Weber, Marcus}, title = {A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations}, volume = {126}, journal = {Journal of Chemical Physics}, number = {2}, doi = {10.1063/1.2404953}, year = {2007}, language = {en} } @article{LasserRoeblitz2010, author = {Lasser, Caroline and R{\"o}blitz, Susanna}, title = {Computing expectation values for molecular quantum dynamics}, volume = {32}, journal = {SIAM Journal on Scientific Computing}, number = {3}, doi = {/10.1137/090770461}, pages = {1465 -- 1483}, year = {2010}, language = {en} } @inproceedings{WeberKube2005, author = {Weber, Marcus and Kube, Susanna}, title = {Robust Perron Cluster Analysis for Various Applications in Computational Life Science}, booktitle = {Computational Life Sciences}, pages = {57 -- 66}, year = {2005}, language = {en} } @inproceedings{KubeWeber2008, author = {Kube, Susanna and Weber, Marcus}, title = {Computation of equilibrium densities in metastable dynamical systems by domain decomposition}, volume = {1048}, booktitle = {Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008}, publisher = {AIP Conference Proceedings}, pages = {339 -- 342}, year = {2008}, language = {en} } @phdthesis{Reinecke2009, author = {Reinecke, Isabel}, title = {Mathematical modeling and simulation of the female menstrual cycle}, year = {2009}, language = {en} } @article{DierkesRoeblitzWadeetal.2013, author = {Dierkes, Thomas and R{\"o}blitz, Susanna and Wade, Moritz and Deuflhard, Peter}, title = {Parameter identification in large kinetic networks with BioPARKIN}, volume = {abs/1303.4928}, journal = {CoRR - Computing Research Repository - arXiv.org}, year = {2013}, language = {en} } @article{RoeblitzStoetzelDeuflhardetal.2013, author = {R{\"o}blitz, Susanna and St{\"o}tzel, Claudia and Deuflhard, Peter and Jones, Hannah M. and Azulay, David-Olivier and van der Graaf, Piet and Martin, Steven}, title = {A mathematical model of the human menstrual cycle for the administration of GnRH analogues}, volume = {321}, journal = {Journal of Theoretical Biology}, doi = {10.1016/j.jtbi.2012.11.020}, pages = {8 -- 27}, year = {2013}, language = {en} } @article{StoetzelPloentzkeHeuwieseretal.2012, author = {St{\"o}tzel, Claudia and Pl{\"o}ntzke, Julia and Heuwieser, Wolfgang and R{\"o}blitz, Susanna}, title = {Advances in modelling of the bovine estrous cycle: Synchronization with PGF2alpha}, volume = {78}, journal = {Theriogenology}, doi = {10.1016/j.theriogenology.2012.04.017}, pages = {1415 -- 1428}, year = {2012}, language = {en} } @article{BoethDudaHelleretal.2013, author = {Boeth, Heide and Duda, Georg and Heller, Markus O. and Ehrig, Rainald and Doyscher, Ralf and Jung, Tobias and Moewis, Philippe and Scheffler, Sven and Taylor, William R.}, title = {Anterior cruciate ligament-deficient patients with passive knee joint laxity have a decreased range of anterior-posterior motion during active movements}, volume = {41}, journal = {The American Journal of Sports Medicine}, number = {5}, doi = {10.1177/0363546513480465}, pages = {1051 -- 7}, year = {2013}, language = {en} } @inproceedings{KubeWeber2008, author = {Kube, Susanna and Weber, Marcus}, title = {Preserving the Markov Property of Reduced Reversible Markov Chains}, volume = {1048}, booktitle = {Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008}, pages = {593 -- 596}, year = {2008}, language = {en} } @article{WeberKubeWalteretal.2007, author = {Weber, Marcus and Kube, Susanna and Walter, Lionel and Deuflhard, Peter}, title = {Stable Computation of Probability Densities of Metastable Dynamical Systems}, volume = {6}, journal = {SIAM J. Multiscale Model. Simul.}, number = {2}, pages = {396 -- 416}, year = {2007}, language = {en} } @article{KratzensteinKornaropoulosEhrigetal.2012, author = {Kratzenstein, Stefan and Kornaropoulos, Evgenios I. and Ehrig, Rainald and Heller, Markus O. and P{\"o}pplau, Berry M. and Taylor, William R.}, title = {Effective marker placement for functional identification of the centre of rotation at the hip}, volume = {36}, journal = {Gait \& Posture}, number = {3}, doi = {http://dx.doi.org/10.1016/j.gaitpost.2012.04.011}, pages = {482 -- 486}, year = {2012}, language = {en} } @inproceedings{TaylorFroehlichButtgereitetal.2012, author = {Taylor, William R. and Fr{\"o}hlich, Annika and Buttgereit, Frank and Ehrig, Rainald and Witaschek, Tom and Duda, Georg}, title = {Metacarpophalangeal joint stiffness is reduced in patients affected by rheumatoid arthritis after glucocorticoid medication}, booktitle = {Proceedings of the ESM-2012, Aalborg}, editor = {Kersting, Uwe and Morlock, Michael and Jirova-Enzmann, Daniela and Dremstrup, Kim}, publisher = {Department of Health Science and Technology, Aalborg University}, pages = {39}, year = {2012}, language = {en} } @article{KubeLasserWeber2008, author = {Kube, Susanna and Lasser, Caroline and Weber, Marcus}, title = {Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics}, volume = {228}, journal = {Journal of Computational Physics}, number = {6}, doi = {10.1016/j.jcp.2008.11.016}, pages = {1947 -- 1962}, year = {2008}, language = {en} } @article{DeuflhardRoeblitzStoetzel2010, author = {Deuflhard, Peter and R{\"o}blitz, Susanna and St{\"o}tzel, Claudia}, title = {Mathematical Systems Biology at Zuse Institute Berlin (ZIB)}, volume = {39}, journal = {BioTOPics - Journal of Biotechnology in Berlin-Brandenburg}, year = {2010}, language = {en} } @article{RoeblitzWeber2009, author = {R{\"o}blitz, Susanna and Weber, Marcus}, title = {Fuzzy Spectral Clustering by PCCA+}, journal = {Classification and Clustering: Models, Software and Applications}, number = {WIAS Report No. 26}, pages = {73 -- 79}, year = {2009}, language = {en} } @misc{Brueggemann2013, type = {Master Thesis}, author = {Br{\"u}ggemann, Jo Andrea}, title = {Numerical Modelling of the human menstrual cycle applied to ovulation prediction}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-46168}, year = {2013}, abstract = {In this Master Thesis, the modelling process and the required biological background to adequately describe the hormonal dynamics of the human menstrual cycle are presented. The aim of this Master thesis project is to establish a mathematical routine that enables prediction of potentially fertile time windows. A system of four parameter dependent ordinary differential equations coupled with two algebraic equations is built, accounting for the main kinetic drivers of the human menstrual cycle { basal body temperature, estradiol, progesterone, luteinizing and follicle stimulating hormone. The key parameters are identifed using a nonlinear least squares approach to match the model to individual data. Aiming to solve the optimality problem arising, the Newton and Gauss-Newton method are examined and their local convergence theory is outlined. By the nature of the application, a globalised Gauss-Newton method seems more convenient. An adaptive trust region approach to determine the step lengths is chosen, which together with an linearly-implicit Euler extrapolation for the given differential algebraic equation system makes parameter estimation possible. The simulation results are discussed particularly in view of limitations and problems arising through the modelling approach.}, language = {en} } @misc{Knoechel2014, type = {Master Thesis}, author = {Kn{\"o}chel, Jane}, title = {Mathematische Modellierung metabolischer Einflussfaktoren auf den Milchkuhzyklus}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-46170}, year = {2014}, abstract = {In den letzten Jahren ist die reproduktive Leistung von Milchk{\"u}hen parallel zur steigenden Milchleistung drastisch gesunken. Um die zu Grunde liegenden biologischen Mechanismen besser zu verstehen, wurde in dieser Arbeit eine Modellerweiterung des vorhandenen Modells von St{\"o}tzel et al. (2011) um metabolische Einflussfaktoren angestrebt. Hierf{\"u}r wurde zuerst aus ver{\"o}ffentlichten, experimentell gewonnen Erkenntnissen herausgearbeitet, wie die metabolischen Faktoren auf das periodische Zyklusverfahren der Milchkuh Einfluss nehmen. Daraus wurde ersichtlich, dass Glukose, Insulin und IGF-I die wichtigsten metabolischen Faktoren sind, aber lediglich IGF-I als dynamische Gr{\"o}ße in das Modell eingeht. Zur Validierung des erweiterten Modells, wurden im Rahmen dieser Arbeit Szenarien aus der Literatur entwickelt, welche eine negative Energiebilanz oder den Effekt von Di{\"a}trestriktionen auf den Milchkuhzyklus simulieren sollten. Ferner wurden Messdaten f{\"u}r IGF, E2 und P4 von Kawashima et al. (2007) und Cerri et al. (2011) bereit gestellt. Das erweiterte Modell umfasst lediglich 8 Parameter mehr als das Ursprungsmodell, wobei gezeigt werden konnte, dass weder die Bedingung f{\"u}r die L{\"o}sbarkeit noch die Stabilit{\"a}t in den Anfangswerten eingeb{\"u}ßt wurde. Die Modellkurven konnten mittels des NLSCON erfolgreich an die bereitgestellten Messdaten f{\"u}r IGF, E2 und P4 angepasst werden. Anhand der Ergebnisse aus den Szenarien ließ sich zeigen, dass es teilweise gelingt {\"u}ber die metabolischen Einflussfaktoren eine negative Energiebilanz f{\"u}r unterern{\"a}hrte K{\"u}he darzustellen. Die R{\"u}ckf{\"u}hrung in das periodische Zyklusverhalten verlief jedoch im Vergleich zu in vivo Beobachtungen zu schnell ab. Eine m{\"o}gliche Erkl{\"a}rung hierf{\"u}r ist ein zu geringer Einfluss von IGF-I auf das Modell. Dar{\"u}ber hinaus kam es trotz (stark) reduzierter LH-Konzentration zur Ovulation. Auf diesen Erkenntnissen aufbauend k{\"o}nnte in Zukunft die Follikelmodellierung modifiziert oder die Hillfunktion, die die Ovulation darstellt, {\"u}berarbeitet werden.}, language = {de} } @misc{Berg2012, type = {Master Thesis}, author = {Berg, Mascha}, title = {Laufzeitoptimierung der Robusten Perron Cluster Analyse (PCCA+)}, year = {2012}, language = {de} }