@misc{DeuflhardHuisingaJahnkeetal., author = {Deuflhard, Peter and Huisinga, Wilhelm and Jahnke, Tobias and Wulkow, Michael}, title = {Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9471}, number = {07-04}, abstract = {\begin{abstract} In systems biology, the stochastic description of biochemical reaction kinetics is increasingly being employed to model gene regulatory networks and signalling pathways. Mathematically speaking, such models require the numerical solution of the underlying evolution equat ion, also known as the chemical master equation (CME). Up to now, the CME has almost exclusively been treated by Monte-Carlo techniques, the most prominent of which is the simulation algorithm suggest ed by Gillespie in 1976. Since this algorithm requires an update for each single reaction event, realizations can be computationally very costly. As an alternative, we here propose a novel approach, which focuses on the discrete partial differential equation (PDE) structure of the CME and thus allows to adopt ideas from adaptive discrete Galerkin methods (as designed by two of the present authors in 1989), which have proven to be highly efficient in the mathematical modelling of polyreaction kinetics. Among the two different options of discretizing the CME as a discrete PDE, the method of lines approach (first space, then time) and the Rothe method (first time, then space), we select the latter one for clear theoretical and algorithmic reasons. First numeric al experiments at a challenging model problem illustrate the promising features of the proposed method and, at the same time, indicate lines of necessary further research. \end{abstract}}, language = {en} } @article{WeiserDeuflhard2007, author = {Weiser, Martin and Deuflhard, Peter}, title = {Inexact central path following algorithms for optimal control problems}, series = {SIAM J. Control Opt.}, volume = {46}, journal = {SIAM J. Control Opt.}, number = {3}, pages = {792 -- 815}, year = {2007}, language = {en} } @article{ReineckeDeuflhard2007, author = {Reinecke, Isabel and Deuflhard, Peter}, title = {A Complex Mathematical Model of the Human Menstrual Cycle}, series = {Journal of Theoretical Biology}, volume = {247}, journal = {Journal of Theoretical Biology}, number = {2}, pages = {303 -- 330}, year = {2007}, language = {en} } @incollection{Deuflhard2007, author = {Deuflhard, Peter}, title = {Painters, Murderers, Mathematicians}, series = {Mathematics and Culture in Europe. Mathematics in Art, Technology, Cinema, and Theatre}, booktitle = {Mathematics and Culture in Europe. Mathematics in Art, Technology, Cinema, and Theatre}, publisher = {Springer-Verlag}, pages = {141 -- 152}, year = {2007}, language = {en} } @article{DeuflhardKrauseErtel2007, author = {Deuflhard, Peter and Krause, Rolf and Ertel, Susanne}, title = {A Contact-Stabilized Newmark Method for Dynamical Contact Problems}, series = {International Journal for Numerical Methods in Engineering}, volume = {73}, journal = {International Journal for Numerical Methods in Engineering}, number = {9}, pages = {1274 -- 1290}, year = {2007}, 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}, series = {SIAM J. Multiscale Model. Simul.}, volume = {6}, journal = {SIAM J. Multiscale Model. Simul.}, number = {2}, pages = {396 -- 416}, year = {2007}, language = {en} } @article{WeiserDeuflhardErdmann2007, author = {Weiser, Martin and Deuflhard, Peter and Erdmann, Bodo}, title = {Affine conjugate adaptive Newton methods for nonlinear elastomechanics}, series = {Opt. Meth. Softw.}, volume = {22}, journal = {Opt. Meth. Softw.}, number = {3}, pages = {413 -- 431}, year = {2007}, language = {en} } @article{WixSchaberOfenlochetal.2007, author = {Wix, A. and Schaber, Karlheinz and Ofenloch, O. and Ehrig, Rainald and Deuflhard, Peter}, title = {Simulation of Aerosol Formation in Gas-Liquid Contact Devices}, series = {Chem. Eng. Comm.}, volume = {194}, journal = {Chem. Eng. Comm.}, pages = {565 -- 577}, year = {2007}, language = {en} }