Repository: Freie Universität Berlin, Math Department

all

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Date | Creators | Item Type | No Grouping
Jump to: 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | 1989 | 1988
Number of items at this level: 391.

2017

Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105 (In Press)

Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2017) The interface for functions in the dune-functions module. Archive of Numerical Software, 5 (1). pp. 95-110. ISSN 2197-8263

Gräser, C. and Kies, T. (2017) Discretization Error Estimates for Penalty Formulations of a Linearized Canham-Helfrich Type Energy. SFB 1114 Preprint .

Huttary, R. and Goubergrits, L. and Schütte, Ch. and Bernhard, S. (2017) Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling. Computers in Biology and Medicine . ISSN 0010-4825 (In Press)

Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence . (In Press)

Kornhuber, R. and Podlesny, J. and Yserentant, H. (2017) Direct and Iterative Methods for Numerical Homogenization. In: Domain Decomposition Methods in Science and Engineering. Lecture Notes in Computational Science and Engineering, XXIII (116). SpringerLink, pp. 217-225. ISBN 978-3-319-52389-7

Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 4701-4709. ISSN 1463-9076

Rath , B. and Conrad, T. O. F. and Myles, P. and Alchikh, M. and Ma, X. and Hoppe, Ch. and Tief, F. and Obermeier, P. and Reiche, J. and Kisler, B. and Schweiger, B. (2017) Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Review of Anti-infective Therapy (IERZ), 15 (6). pp. 545-568.

Rüderich, Stefan and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for finding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press)

Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250.

Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154

2016

Babushkina, E. and Kornhuber, R. (2016) Adaptive multilevel Monte Carlo methods for stochastic variational inequalities. arXiv:1611.06012 . (Submitted)

Banisch, Ralf and Hartmann, C. (2016) A sparse Markov chain approximation of LQ-type stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363-389. ISSN 1064-8275

Blatt, M. and Burchardt, A. and Dedner, A. and Engwer, C. and Fahlke, J. and Flemisch, B. and Gersbacher, C. and Gräser, C. and Gruber, F. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Malkmus, T. and Müthing, S. and Nolte, M. and Piatkowski, M. and Sander, O. (2016) The Distributed and Unified Numerics Environment, Version 2.4. Archive of Numerical Software, 4 (100). pp. 13-29. ISSN 2197-8263

Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130).

Gelß, P. and Matera, S. and Schütte, Ch. (2016) Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model. Journal of Computational Physics, 314 . pp. 489-502. ISSN 0021-9991

Gräser, C. and Kahnt, M. and Kornhuber, R. (2016) Numerical approximation of multi-phase Penrose-Fife systems. Computational Methods in Applied Mathematics, 16 (4). pp. 523-542. ISSN Online: 1609-9389, Print: 1609-4840

Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715

Hoppe, C. and Obermeier, P. and Muehlhans, S. and Alchikh, M. and Seeber, L. and Tief, F. and Karsch, K. and Chen, X. and Boettcher, S. and Diedrich, S. and Conrad, T. O. F. and Kisler, B. and Rath , B. (2016) Article: Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study. Drug Safety, 39 (10). pp. 977-988. ISSN 1179-1942

Kornhuber, R. and Peterseim, D. and Yserentant, H. (2016) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation . ISSN 0025-5718 (In Press)

Mireles, Victor and Conrad, T. O. F. (2016) Decomposing biological systems into reusable modules reveals characteristic module size distributions. n/a . (Submitted)

Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196.

Rams, Mona (2016) A new approach for biomarker detection using fusion networks. Masters thesis, Freie Universität Berlin.

Shao, Borong and Conrad, T. O. F. (2016) Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction. Lecture Notes in Computer Science (LNCS): Proceeding of IWBBIO 2016, 9656 .

Stolzenberg, S. and Michino, M. and LeVine, M. and Weinstein, H. and Shi, L. (2016) Computational approaches to detect allosteric pathways in transmembrane molecular machines. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (7). p. 1652. ISSN 00052736

Tief, F. and Hoppe, Ch. and Seeber, L. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, T. O. F. and Schweiger, B. and Adam, T. and Rath , B. (2016) An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use. Antiviral Therapy, 21 (5). pp. 413-424. ISSN 1359-6535 (print); 2040-2058 (online)

Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 .

You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322

Youett, J. and Sander, O. and Kornhuber, R. (2016) A globally convergent filter-trust-region method for large deformation contact problems. Preprint 1116, Matheon Berlin . (Submitted)

2015

Deckelnick, K. and Elliott, C.M. and Kornhuber, R. and Sethian, J. A., eds. (2015) Geometric partial differential equations: Surface and bulk processes. Oberwolfach Reports, 12 (4). European Mathematical Society - Publishing House, Zürich, Switzerland.

Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606

Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630

Akyuz, N. and Georgieva, E. R. and Zhou, Z. and Stolzenberg, S. and Cuendet, M. A. and Khelashvili, G. and Altman, R. B. and Terry, D. S. and Freed, J. H. and Weinstein, H. and Boudker, O. and Blanchard, S. (2015) Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature, 518 (7537). p. 68. ISSN 0028-0836

Babushkina, E. S. and Bessonov, N. M. and Ataullakhanov, F. I. and Panteleev, M. A. (2015) Continuous modeling of arterial platelet thrombus formation using a spatial adsorption equation. PLoS ONE, 10 (10). ISSN 1932-6203

Banisch, Ralf and Djurdjevac, N. (2015) Cycle-flow–based module detection in directed recurrence networks. EPL (Europhysics Letters) , 108 (6). ISSN 0295-5075

Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355

Billesbølle, C. B. and Krüger, M. B. and Shi, L. and Quick, M. and Li, Z. and Stolzenberg, S. and Kniazeff, J. and Gotfryd, K. and Mortensen, J. S. and Javitch, J. A. and Weinstein, H. and Loland, C.J. and Gether, U. (2015) Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter. Journal of Biological Chemistry, 290 (44). p. 26725. ISSN 0021-9258

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355

Bittracher, Andreas and Koltai, Péter and Junge, Oliver (2015) Pseudogenerators of spatial transfer operators. SIAM Journal on Applied Dynamical Systems, 14 (3). pp. 1478-1517. ISSN 1536-0040

Deuflhard, P. and Röblitz, S. (2015) A Guide to Numerical Modelling in Systems Biology. Texts in Computational Science and Engineering, 12 . Springer International Publishing, Basel. ISBN 978-3-319-20058-3 (print) / 978-3-319-20059-0 (online)

Djurdjevac, N. and Banisch, Ralf and Schütte, Ch. (2015) Modularity of Directed Networks: Cycle Decomposition Approach. Journal of Computational Dynamics, 2 (1). pp. 1-24. ISSN 2158-2491

Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200.

Ehrig, R. and Dierkes, T. and Schäfer, S. and Röblitz, S. and Tronci, E. and Mancini, T. and Salvo, I. and Alimguzhin, V. and Mari, F. and Melatti, I. and Massini, A. and Krüger, T. H. C. and Egli, M. and Ille, F. and Leeners, B. (2015) An integrative approach for model driven computation of treatments in reproductive medicine. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606

Grohs, P. and Hardering, H. and Sander, O. (2015) Optimal a priori discretization error bounds for geodesic finite elements. Foundations of Computational Mathematics, 15 (6). pp. 1357-1411. ISSN 1615-3375

Gräser, C. (2015) A note on Poincaré- and Friedrichs-type inequalities. arXiv:1512.02842 . (Submitted)

Gräser, C. and Kornhuber, R. and Sack, U. (2015) Nonsmooth Schur-Newton methods for multicomponent Cahn-Hilliard systems. IMA Journal of Numerical Analysis, 35 (2). pp. 652-679. ISSN 0272-4979

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2015) Importance sampling in path space for diffusion processes. Probab. Theory Rel. Fields . (Submitted)

Karsch, K. and Obermeier, P. and Seeber, L. and Chen, X. and Tief, F. and Muehlhans, S. and Hoppe, Ch. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2015) Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children. The Pediatric Infectious Disease Journal, 34 (10).

Lenga, Matthias and Conrad, T. O. F. (2015) Non-convex regularization for supervised learning. Technical Report . (Unpublished)

Mireles, Victor and Conrad, T. O. F. (2015) Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrices. Procedia Computer Science, 51 . pp. 2967-2971. ISSN 1877-0509

Moualeu-Ngangue, D. P. and Röblitz, S. and Ehrig, R. and Deuflhard, P. (2015) Parameter Identification in a Tuberculosis Model for Cameroon. PLoS ONE, 10 (4). e0120607. ISSN 1932-6203

Ozdoba, Christopher (2015) Ensemble Machine Learning Techniques for Analyzing Large Biological Datasets Using the SAP In-Memory Database HANA. Masters thesis, Freie Universität Berlin.

Pipping, E. and Sander, O. and Kornhuber, R. (2015) Variational formulation of rate- and state-dependent friction problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 95 (4). pp. 377-395. ISSN 0044-2267

Plöntzke, J. and Berg, M. and Stötzel, C. and Röblitz, S. (2015) A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064

Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355

Shao, Borong and Conrad, T. O. F. (2015) Are NoSQL data stores useful for bioinformatics researchers? "International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), 3 (3). pp. 1704-1708. ISSN 2321-8169

Stolzenberg, S. and Quick, M. and Zhao, C. and Gotfryd, K. and Khelashvili, G. and Gether, U. and Loland, C. J. and Javitch, J. A. and Noskov, S. and Weinstein, H. and Shi, L. (2015) Mechanism of the Association between Na+Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. Journal of Biological Chemistry, 290 (22). p. 13992. ISSN 0021-9258

Stötzel, C. and Ehrig, R. and Boer, H.M.T. and Plöntzke, J. and Röblitz, S. (2015) Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis. In: BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, 02.11.2014 - 08.11.2014, Bedlewo - Poland.

Stötzel, C. and Röblitz, S. and Siebert, H. (2015) Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation. PLoS ONE, 10 (10). e0140954. ISSN 1932-6203

Wallmeyer, Leonie and Rams, Mona and Börno, Stefan and Timmermann, Bernd and Hedtrich, Sarah and Conrad, T. O. F. (2015) Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach. Technical Report . (Unpublished)

You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished)

Zhang, W. and Hartmann, C. and von Kleist, M. (2015) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. SIAM Multiscale Modeling & Simulation . ISSN print: 1540-3459; online: 1540-3467 (Submitted)

2014

Bach, V. and Delle Site, L., eds. (2014) Many-Electron Approaches in Physics, Chemistry and Mathematics. Mathematical Physics Studies . Springer, Heidelberg. ISBN 978-3-319-06378-2

Agarwal, A. and Wang, H. and Schütte, Ch. and Delle Site, L. (2014) Chemical potential of liquids and mixtures via Adaptive Resolution Simulation. Journal of Chemical Physics, 141 (3). ISSN 0021-9606

Berninger, H. and Loisel, S. and Sander, O. (2014) The 2-Lagrange multiplier method applied to nonlinear transmission problems for the Richards equation in heterogeneous soil with cross points. SIAM J. Sci. Comput., 36 (5). A2166-A2198. ISSN 1064-8275

Berninger, H. and Ohlberger, M. and Sander, O. and Smetana, K. (2014) Unsaturated subsurface flow with surface water and nonlinear in- and outflow conditions. Mathematical Models and Methods in Applied Sciences, 24 (5). pp. 901-936. ISSN 1793-6314

Gräser, C. and Kornhuber, R. and Sack, U. (2014) Numerical simulation of coarsening in binary solder alloys. Computational Materials Science, 93 . pp. 221-233. ISSN 0927-0256

Gräser, C. and Sander, O. (2014) Polyhedral Gauß-Seidel converges. Journal of Numerical Mathematics, 22 (3). pp. 221-254. ISSN 1570-2820

Gräser, C. and Sander, O. (2014) Truncated nonsmooth Newton multigrid methods for simplex-constrained minimization problems. Preprint 384, IGPM Aachen . (Submitted)

Hédin, F. and Plattner, N. and Doll, J. D. and Meuwly, M. (2014) Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. Journal of Chemical Theory and Computation, 10 (10). pp. 4284-4296. ISSN 1549-9618

Jouvet, G. and Funk, M. (2014) Modelling the trajectory of the corpses of mountaineers who disappeared in 1926 on Aletschgletscher, Switzerland. Journal of Glaciology, 60 (220). pp. 255-261. ISSN 0022-1430

Jouvet, G. and Rappaz, J. (2014) Numerical analysis and simulation of the dynamics of mountain glaciers. In: Modeling, Simulation and Optimization for Science and Technology. Computational Methods in Applied Sciences (34). Springer Netherlands, pp. 83-92. ISBN 978-94-017-9053-6

Kabbe, G. and Wehmeyer, C. and Sebastiani, D. (2014) A Coupled Molecular Dynamics/Kinetic Monte Carlo Approach for Protonation Dynamics in Extended Systems. Journal of Chemical Theory and Computation, 10 (10). p. 4221. ISSN 1549-9618

Kornhuber, R. and Schwab, C. and Wolf, M.W. (2014) Multilevel Monte Carlo finite element methods for stochastic elliptic variational inequalities. SIAM Journal on Numerical Analysis, 52 (3). pp. 1243-1268. ISSN 0036-1429

Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted)

Meixenberger, K. and Hauser, A. and Jansen, K. and Yousef, K. P. and Fiedler, S. and von Kleist, M. and Norley, S. and Somogyi, S. and Hamouda, O. and Bannert, N. and Bartmeyer, B. and Kücherer, C. (2014) Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker to identify recent infections in HIV-1 incidence studies. Journal of Clinical Microbiology, 52 (8). pp. 2977-2983. ISSN 0095-1137

Sander, O. and Schiela, A. (2014) Variational analysis of the coupling between a geometrically exact Cosserat rod and an elastic continuum. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 65 (6). pp. 1261-1288. ISSN 0044-2275 (Print) 1420-9039 (Online)

Sarich, M. and Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2014) Modularity revisited: A novel dynamics-based concept for decomposing complex networks. Journal of Computational Dynamics, 1 (1). pp. 191-212. ISSN 2158-2491

Vetter, A. and Sander, O. and Duda, G. and Weinkamer, R. (2014) Healing of a mechano-responsive material. Europhysics Letters (EPL), 104 (6). pp. 1-6. ISSN 0295-5075

Wang, H. and Schütte, Ch. and Ciccotti, G. and Delle Site, L. (2014) Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation. Journal of Chemical Theory and Computation, 10 (4). pp. 1376-1386. ISSN 1549-9618

von Rudorff, G. F. and Wehmeyer, C. and Sebastiani, D. (2014) Efficient implementation and application of the artificial bee colony algorithm to low-dimensional optimization problems. Computer Physics Communications, 185 (6). p. 1639. ISSN 00104655

2013

Berninger, H. and Kornhuber, R. and Sander, O. (2013) Heterogeneous substructuring methods for coupled surface and subsurface flow. In: Domain Decomposition Methods in Science and Engineering XX. Lecture Notes in Computational Science and Engineering, 91 . Springer Berlin Heidelberg, pp. 427-434. ISBN 978-3-642-35274-4

Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743

Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976

Gräser, C. (2013) Nonsmooth Schur-Newton methods for nonsmooth saddle point problems. Preprint 1004, Matheon Berlin .

Gräser, C. and Kornhuber, R. and Sack, U. (2013) Time discretizations of anisotropic Allen-Cahn equations. IMA Journal of Numerical Analysis, 33 (4). pp. 1226-1244. ISSN 0272-4979

Gul, Rahim and Bernhard, Stefan (2013) Local sensitivity analysis of cardiovascular system parameters. International Journal of Scientific and Engineering Research (IJSER), 4 (7). pp. 2648-2661. ISSN 2229-5518

Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36).

Hardering, H. (2013) Numerical approximation of capillary surfaces in a negative gravitational field. Interfaces and Free Boundaries, 15 (3). pp. 263-280. ISSN 1463-9971

Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2013) Characterization of Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 350-376. ISSN 1099-4300

Hartmann, C. and Schäfer-Bung, B. and Thöns-Zueva, A. (2013) Balanced averaging of bilinear systems with applications to stochastic control. SIAM J. Control Optim., 51 (3). pp. 2356-2378.

Hartmann, C. and Yanao, Tomohiro (2013) The falling cat problem and shape effects in small molecules in a random environment: a case study. Molecular Physics, 111 (22-23). pp. 3534-3545. ISSN 0026-8976

Jouvet, G. and Bueler, E. and Gräser, C. and Kornhuber, R. (2013) A nonsmooth Newton multigrid method for a hybrid, shallow model of marine ice sheets. Recent Advances in Scientific Computing and Applications, 586 . pp. 208-217. ISSN 0271-4132

Jouvet, G. and Gräser, C. (2013) An adaptive Newton multigrid method for a model of marine ice sheets. Journal of Computational Physics, 252 . pp. 419-437. ISSN 0021-9991

Kantcheva, A. K. and Quick, M. and Shi, L. and Winther, A.-M. L. and Stolzenberg, S. and Weinstein, H. and Javitch, J. A. and Nissen, P. (2013) Chloride binding site of neurotransmitter sodium symporters. Proceedings of the National Academy of Sciences, 110 (21). p. 8489. ISSN 0027-8424

Leichtle, A. and Ceglarek, U. and Weinert, P. and Nakas, C. T. and Nuoffer, J.-M. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2013) Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma. Metabolomics, 9 (3). pp. 677-687. ISSN 1573-3890

Pattyn, F. and Perichon, L. and Durand, G. and Favier, L. and Gagliardini, O. and Hindmarsh, R. and Zwinger, T. and Albrecht, T. and Cornford, S. and Docquier, D. and Fuerst, J. and Goldberg, G. and Gudmundsson, G. H. and Humbert, A. and Huetten, M. and Huybrechts, P. and Jouvet, G. and Kleiner, T. and Larour, E. and Martin, D. (2013) Grounding-line migration in plan-view marine ice-sheet models: Results of the ice2sea MISMIP3d intercomparison. Journal of Glaciology, 59 (215). pp. 410-422. ISSN 0022-1430

Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297

Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir. Infectious Disorders - Drug Targets, 13 (1). pp. 25-33. ISSN 2212-3989

Sander, O. (2013) Coupling geometrically exact cosserat rods and linear elastic continua. In: Domain Decomposition Methods in Science and Engineering XX. Lecture Notes in Computational Science and Engineering, 91 . Springer Berlin Heidelberg, pp. 443-450. ISBN 978-3-642-35274-4

Sander, O. (2013) Geodesic finite elements in spaces of zero curvature. In: Numerical Mathematics and Advanced Applications 2011. Proceedings of ENUMATH 2011, the 9th European Conference on Numerical Mathematics and Advanced Applications, Leicester, September 2011 . Springer Berlin Heidelberg, pp. 449-457. ISBN 978-3-642-33133-6

Sander, O. and Klapproth, C. and Youett, J. and Kornhuber, R. and Deuflhard, P. (2013) Towards an efficient numerical simulation of complex 3D knee joint motion. Computing and Visualization in Science, 16 (3). pp. 119-138. ISSN 1432-9360

Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300

Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976

Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018.

Wehmeyer, C and Schrader, M and Andrienko, D and Sebastiani, D (2013) Water-Free Proton Conduction in Hexakis(p-Phosphonatophenyl)benzene Nanochannels. The Journal of Physical Chemistry C, 117 (23). p. 12366. ISSN 1932-7447

2012

Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203

Bastian, P. and Berninger, H. and Dedner, A. and Engwer, C. and Henning, P. and Kornhuber, R. and Kröner, D. and Ohlberger, M. and Sander, O. and Schiffler, G. and Shokina, N. and Smetana, K. (2012) Adaptive modelling of coupled hydrological processes with application in water management. In: Progress in Industrial Mathematics at ECMI 2010. Mathematics in Industry: The European Consortium for Mathematics in Industry (17). Springer Berlin Heidelberg, pp. 561-567. ISBN 978-3-642-25100-9

Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81.

Gupta, Pooja and Conrad, T. O. F. and Spötter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar (2012) Simulating a base population in honey bee for molecular genetic studies. Genetics Selection Evolution, 44 . p. 14.

Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004.

Jouvet, G. and Bueler, E. (2012) Steady, shallow ice sheets as obstacle problems: Well-posedness and finite element approximation. SIAM J. Appl. Math., 72 (4). pp. 1292-1314. ISSN 0036-1399

Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890

Menz, S. and Latorre, J.C. and Schütte, Ch. and Huisinga, W. (2012) Hybrid Stochastic–Deterministic Solution of the Chemical Master Equation. SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS), 10 (4). pp. 1232-1262.

Sander, O. (2012) Geodesic finite elements on simplicial grids. International Journal for Numerical Methods in Engeneering, 92 (12). pp. 999-1025. ISSN Online: 1097-0207

Sander, O. and Schiela, A. (2012) Energy minimizers of the coupling of a Cosserat rod to an elastic continuum. Mathematical Modelling, 7 (1). pp. 1118-1123.

Stolzenberg, S. and Khelashvili, G. and Weinstein, H. (2012) Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh. The Journal of Physical Chemistry B, 116 (18). p. 5372. ISSN 1520-6106

Vetter, A. and Witt, F. and Sander, O. and Duda, G. and Weinkamer, E. (2012) The spatio-temporal arrangement of different tissues during bone healing as a result of simple mechanobiological rules. Biomechanics and Modeling in Mechanobiology, 11 (1-2). pp. 147-160. ISSN 1617-7959

Wehmeyer, C. and Falk von Rudorff, G. and Wolf, S. and Kabbe, G. and Schärf, D. and Kühne, T. D. and Sebastiani, D. (2012) Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry. The Journal of Chemical Physics, 137 (19). p. 194110. ISSN 00219606

Youett, J. and Sander, O. (2012) A dissipative discretization for large deformation frictionless dynamic contact problems. MATHEON Preprint #1184 .

2011

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Convergence behaviour of Dirichlet-Neumann and Robin methods for a nonlinear transmission problem. In: Domain Decomposition Methods in Science and Engineering XIX. Lecture Notes in Computational Science and Engineering, 78 . Springer Berlin Heidelberg, pp. 87-98. ISBN 978-3-642-11303-1

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Fast and robust numerical solution of the Richards equation in homogeneous soil. SIAM Journal on Numerical Analysis, 49 (6). pp. 2576-2597. ISSN 0036-1429

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Heterogeneous domain decomposition of surface and porous media flow. AIP Conference Proceedings, 1389 . pp. 2025-2028. ISSN 0094-243X

Dziuk, G. and Elliott, C.M. and Huisken, G. and Kornhuber, R. (2011) Geometric partial differential equations: Theory, numerics and applications. Oberwolfach Reports, 8 (4). European Mathematical Society.

Han, D. S. and Golebiewska, U. and Stolzenberg, S. and Scarlata, S. F. and Weinstein, H. (2011) A Dynamic Model of Membrane-Bound Phospholipase C 2 Activation by G Subunits. Molecular Pharmacology, 80 (3). p. 434. ISSN 0026-895X

Hartmann, C. (2011) Balanced model reduction of partially-observed Langevin processes: an averaging principle. Math. Comput. Model. Dyn. Syst., 17 (5). pp. 463-490.

Hartmann, C. and Latorre, J.C. and Ciccotti, G. (2011) On two possible definitions of the free energy for collective variables. Eur. Phys. J. Special Topics, 200 (1). pp. 73-89.

Ihrig, A C and Schiffmann, C and Sebastiani, D (2011) Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups. The Journal of Chemical Physics, 135 (21). p. 214107. ISSN 00219606

Jouvet, G. and Huss, M. and Funk, M. and Blatter, H. (2011) Modelling the retreat of Grosser Aletschgletscher, Switzerland, in a changing climate. Journal of Glaciology, 57 (206). pp. 1033-1045. ISSN 0022-1430

Jouvet, G. and Rappaz, J. (2011) Analysis and finite element approximation of a nonlinear stationary stokes problem arising in glaciology. Advances in Numerical Analysis, 2011 (Articl). ISSN 1687-9562

Kornhuber, R. and Zou, Q. (2011) Efficient and reliable hierarchical error estimates for the discretization error of elliptic obstacle problems. Mathematics of Computation, 80 . pp. 69-88. ISSN 0025-5718

Latorre, J.C. and Metzner, Ph. and Hartmann, C. and Schütte, Ch. (2011) A Structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci., 9 (4). pp. 1051-1072.

Sander, O. (2011) The PSurface library. Computing and Visualization in Science, 14 (8). pp. 353-370. ISSN 1432-9360

Schiffmann, C and Sebastiani, D (2011) Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. Journal of Chemical Theory and Computation, 7 (5). p. 1307. ISSN 1549-9618

Schiffmann, C and Sebastiani, D (2011) Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy. physica status solidi (b), 249 (2). p. 368. ISSN 03701972

Vetter, A. and Liu, Y. and Witt, F. and Manjubala, I. and Sander, O. and Rao Epari, D. and Fratzl, P. and Duda, G. and Weinkamer, R. (2011) The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing. Journal of Biomechanics, 44 (3). pp. 517-523. ISSN 0021-9290

Zou, Q. and Veeser, A. and Kornhuber, R. and Gräser, C. (2011) Hierarchical error estimates for the energy functional in obstacle problems. Numerische Mathematik, 117 (4). pp. 653-677. ISSN 0029-599X

2010

Bastian, G and Vogelsang, A and Schiffmann, C (2010) Isotopic Superlattices for Perfect Phonon Reflection. Journal of Electronic Materials, 39 (9). p. 1769. ISSN 0361-5235

Bastian, P. and Buse, G. and Sander, O. (2010) Infrastructure for the Coupling of Dune Grids. In: Numerical Mathematics and Advanced Applications 2009: Proceedings of ENUMATH 2009. Springer Berlin Heidelberg, pp. 107-114. ISBN 978-3-642-11794-7

Berninger, H. and Sander, O. (2010) Substructuring of a Signorini-type problem and Robin's method for the Richards equation in heterogeneous soil. Computing and Visualization in Science, 13 (5). pp. 187-205. ISSN 1432-9360

Diederichs, E. and Juditski, A. and Spokoiny, V. and Schütte, Ch. (2010) Sparse Non-Gaussian Component Analysis. IEEE Transactions on Information Theory, 56 (6). pp. 3033-3047. ISSN 0018-9448

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2010) On Markov State Models for Metastable Processes. In: ICM 2010.

Forster, R. and Kornhuber, R. (2010) A polynomial chaos approach to stochastic variational inequalities. Journal of Numerical Mathematics, 18 (4). pp. 235-255. ISSN 1570-2820

Gräser, C. and Kornhuber, R. and Sack, U. (2010) On hierarchical error estimators for time-discretized phase field models. In: Numerical Mathematics and Advanced Applications 2009: Proceedings of ENUMATH 2009. Springer Berlin Heidelberg, pp. 397-405. ISBN 978-3-642-11794-7

Hartmann, C. and Schütte, Ch. and Ciccotti, G. (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys., 132 (11). p. 111103.

Hartmann, C. and Vulcanov, V.-M. and Schütte, Ch. (2010) Balanced Truncation of Second Order Systems: a Hamiltonian approach. Multiscale Model. Simul., 8 (4). pp. 1348-1367.

Horenko, I. (2010) Finite Element Approach to Clustering of Multidimensional Time Series. J. Sci. Comp., 32 (1). pp. 62-83.

Horenko, I. (2010) On Clustering of Non-stationary Meteorological Time Series. Dyn. of Atm. and Oc., 49 (2-3). pp. 164-187.

Kornhuber, R. (2010) Mathematik hilft heilen. In: Wissenschaftsstadt Berlin. Berliner Wirtschaftsgespräche e.V., p. 123.

Latorre, J.C. and Hartmann, C. and Schütte, Ch. (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science, 1 (1). pp. 1591-1600.

Metzner, Ph. and Weber, M. and Schütte, Ch. (2010) Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82 (3). 031114.

Sander, O. and Schmidt, L. and Ehrig, R. and Heller, M. and Taylor, B. and Kornhuber, R. (2010) Numerical determination of the medio-lateral force distribution in an ovine stifle joint. Biomedizinische Technik/Biomedical Engineering: Proceedings of BMT, Rostock, 55 (s1). ISSN 0013-558

Sander, O. (2010) Geodesic finite elements for Cosserat rods. International Journal for Numerical Methods in Engineering, 82 (13). pp. 1645-1670. ISSN 1097-0207

Sarich, M. and Schütte, Ch. and Vanden-Eijnden, E. (2010) Optimal Fuzzy Aggregation of Networks. Multiscale Modeling and Simulation, 8 (4). pp. 1535-1561.

Schiffmann, C and Appert-Rolland, C and Santen, L (2010) Shock dynamics of two-lane driven lattice gases. Journal of Statistical Mechanics: Theory and Experiment, 2010 (06). P06002. ISSN 1742-5468

2009

Bercovier, M. and Gander, M. and Kornhuber, R. and Widlund, O., eds. (2009) Domain decomposition methods in science and engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg. ISBN 978-3-642-02676-8

Barth, I. and Lasser, C. (2009) Trigonometric pulse envelopes for laser-induced quantum dynamics. J. Phys. B: At. Mol. Opt. Phys., 42 (23). p. 235101.

Berninger, H. (2009) Non-overlapping domain decomposition for the Richards equation via superposition operators. In: Domain Decomposition Methods in Science and Engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg, pp. 169-176. ISBN 978-3-642-02676-8

Dittmer, E. (2009) Hidden Markov Models with Time-Continuous Output Behavior. PhD thesis, FU Berlin.

Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432

Franzke, Ch. and Horenko, I. and Majda, A. J. and Klein, R. (2009) Systematic Metastable Atmospheric Regime Identification in an AGCM. J. Atm. Sci., 66 (7). pp. 1997-2012.

Gräfe, Ch. and Nordmeier, V. and Schütte, Ch. (2009) Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels. Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik), 1 . pp. 77-79. ISSN 978-3-643-10010-8

Gräser, C. and Kornhuber, R. (2009) Multigrid methods for obstacle problems. Journal of Computational Mathematics, 27 (1). pp. 1-44. ISSN 0254-9409

Gräser, C. and Kornhuber, R. (2009) Nonsmooth Newton methods for set-valued saddle point problems. SIAM Journal on Numerical Analysis, 47 (2). pp. 1251-1273. ISSN 0036-1429

Gräser, C. and Sack, U. and Kornhuber, R. (2009) Truncated nonsmooth Newton multigrid methods for convex minimization problems. In: Domain Decomposition Methods in Science and Engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg, pp. 129-136. ISBN 978-3-642-02676-8

Gräser, C. and Sander, O. (2009) The dune-subgrid module and some applications. Computing, 86 (4). pp. 269-290. ISSN 0010-485X

Hartmann, C. (2009) Balancing of dissipative Hamiltonian systems. In: Proceedings of MATHMOD 2009; I. Troch, F. Breitenecker (eds.); ARGESIM Report no. 35.

Hartmann, C. and Schütte, Ch. and Kalibaeva, G. and Di Pierro, M. and Ciccotti, G. (2009) Fast Simulation of Polymer Chains. J. Chem. Phys., 130 . p. 144101.

Horenko, I. (2009) On metastable conformational analysis of non-equilibrium biomolecular time series. MMS . (Submitted)

Klein, R. (2009) Asymptotics, structure, and integration of sound-proof atmospheric flow equations. Theoretical and Computational Fluid Dynamics, 23 (3). pp. 161-195. ISSN 0935-4964 (Print) 1432-2250 (Online)

Kube, S. and Lasser, C. and Weber, M. (2009) Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. J. Comp. Phys., 228 (6). pp. 1947-1962.

Meerbach, E. (2009) Off- and Online Detection of Dynamical Phases in Time Series. PhD thesis, Free University of Berlin.

Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106.

Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2009) Transition Path Theory for Markov Jump Processes. Mult. Mod. Sim., 7 (3). pp. 1192-1219.

Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335.

Schütte, Ch. and Jahnke, T. (2009) Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation. Mathematical Modelling and Numerical Analysis (ESAIM), 43 (4). pp. 721-742.

Splettstößer, T. and Noé, F. and Oda, T. and Smith, J. C. (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state. Proteins, 76 . pp. 353-364.

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Miller, K. and Schrader, M. (2009) Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J of Urology, 28 (2). pp. 193-197.

Swart, T. and Rousse, V. (2009) A Mathematical Justification for the Herman-Kluk Propagator. Comm. Math. Phys., 286 (2). pp. 725-750.

2008

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. ISSN 0010-485X

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part I: Abstract framework. Computing, 82 (2-3). pp. 103-119. ISSN 0010-485X

Conrad, T. O. F. and Reinert, K. and Kohlbacher, O. (2008) Bioinformatics Support for Mass Spectrometry Quality Control. In: Proteomics Sample Preparation. Wiley-Vch, p. 485.

Conrad, T. O. F. (2008) New Statistical Algorithms for the Analysis of Mass Spectrometry Time-Of-Flight Mass Data with Applications in Clinical Diagnostics. PhD thesis, Freie Universität Berlin.

Fermanian Kammerer, C. and Lasser, C. (2008) Propagation through Generic Level Crossings: A Surface Hopping Semigroup. J. Math. Anal., 40 (1). pp. 103-133.

Fermanian Kammerer, C. and Lasser, C. (2008) Single switch surface hopping for molecular dynamics with transitions. J. Chem. Phys., 128 (14). p. 144102.

Fischbach, M. (2008) Methods for modeling metastable conformational dynamics from trajectory data. Masters thesis, FU Berlin.

Forster, R. and Kornhuber, R. and Mautner, K. and Sander, O. (2008) Fast and reliable pricing of American options with local volatility. In: Domain Decomposition Methods in Science and Engineering XVII. Lecture Notes in Computational Science and Engineering, 60 . Springer Berlin Heidelberg, pp. 383-390. ISBN 978-3-540-75198-4

Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133.

Gräser, C. (2008) Globalization of nonsmooth Newton methods for optimal control problems. In: Numerical Mathematics and Advanced Applications. Proceedings of ENUMATH 2007, the 7th European Conference on Numerical Mathematics and Advanced Applications, Graz, Austria, September 2007 . Springer Berlin Heidelberg, pp. 605-612. ISBN 978-3-540-69776-3

Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872.

Hartmann, C. (2008) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. J. Stat. Phys., 130 (4). pp. 687-712.

Hartmann, C. (2008) Structure-preserving model reduction of partially observed differential equations: molecular dynamics and beyond. Oberwolfach Reports, 5 (2). pp. 1111-1115.

Horenko, I. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis. Multiscale Modeling & Simulation, 6 (4). p. 1125. ISSN 15403467

Horenko, I. (2008) On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification. J. Atm. Sci, 65 (6). pp. 1941-1954.

Horenko, I. and Dolaptchiev, S. and Eliseev, A. and Mokhov, I. and Klein, R. (2008) Metastable Decomposition of High-Dimensional Meteorological Data with Gaps. Journal of the Atmospheric Sciences, 65 (11). pp. 3479-3496.

Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145.

Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560.

Horenko, I. and Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted)

Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773.

Kornhuber, R. and Krause, R. and Sander, O. and Deuflhard, P. and Ertel, S. (2008) A monotone multigrid solver for two body contact problems in biomechanics. Computing and Visualization in Science, 11 (1). pp. 3-15. ISSN 1432-9360

Kornhuber, R. and Yserentant, H. (2008) Multigrid methods for discrete elliptic problems on triangular surfaces. Computing and Visualization in Science, 11 (4-6). pp. 251-257. ISSN 1432-9360

Lasser, C. and Swart, T. (2008) Single switch surface hopping for a model of pyrazine. J. Chem.Phys., 129 (03). 034302.

Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted .

Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103.

Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162.

Sakalli, I. (2008) Parallelization Strategies for a Brownian Dynamics Algorithm. Other thesis, FU Berlin.

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83.

2007

Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464.

Gräser, C. and Kornhuber, R. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Domain Decomposition Methods in Science and Engineering XVI. Lecture Notes in Computational Science and Engineering, 55 . Springer Berlin Heidelberg, pp. 91-102. ISBN 978-3-540-34468-1

Gu, W. and Frigato, T. and Straatsma, T. P. and Helms, V. (2007) Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew. Chem. Int. Ed., 46 (16). pp. 2939-2943.

Hartmann, C. (2007) Model Reduction in Classical Molecular Dynamics. PhD thesis, Freie Universität Berlin.

Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63.

Held, M. (2007) Conformational Studies of UDP-N-Acetyl-Glucosamine in Environments of Increasing Complexity. Masters thesis, FU Berlin.

Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Schütte, Ch. (2007) Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity. In: From Computational Biophysics to Systems Biology.

Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706.

Jahnke, T. and Huisinga, W. (2007) Solving the Chemical Master Equation for Monomolecular Reaction Systems Analytically. J. Math. Biol., 54 (1). pp. 1-26.

Kiljunen, T. and Schmidt, B. (2007) Alignment and Orientation of Molecules in Matrices. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 337-352.

Kornhuber, R. and Gräser, C. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Decomposition Methods in Science and Engineering XVI. LNCSE (55). Springer, pp. 91-102. ISBN 978-3-540-34469-8

Lasser, C. and Swart, T. and Teufel, St. (2007) Construction and validation of a rigorous surface hopping algorithm for conical crossings. Comm. Math. Sci., 5 (4). pp. 789-814.

Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399.

Meerbach, E. and Schütte, Ch. and Horenko, I. and Schmidt, B. (2007) Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 796-806.

Metzner, Ph. (2007) Transition Path Theory for Markov Processes. PhD thesis, Free University of Berlin.

Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375.

Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702.

Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440.

Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102.

Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se .

von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806.

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

2006

Barth, I. and Gonzalez, L. and Lasser, C. and Manz, J. and Rozgonyi, T. (2006) Laser control of nuclear and electron dynamics: bond selective photodissociation and electron circulation. In: Coherent Control of Molecules. Collaborative Computational Project (6). Daresbury Laboratory, pp. 18-27.

Bastian, P. and Blatt, M. and Engwer, C. and Dedner, A. and Klöfkorn, R. and Kuttanikkad, S. P. and Ohlberger, M. and Sander, O. (2006) The Distributed and Unified Numerics Environment (DUNE). Proc. of the 19th Symposium on Simulation Technique .

Bornemann, F. A. and Lasser, C. and Swart, T. (2006) Energy Level Crossings in Molecular Dynamics. In: Analysis, Modeling and Simulation of Multiscale Problems. Springer, Berlin, pp. 577-594.

Caselles, V. and Igual, L. and Sander, O. (2006) An axiomatic approach to scalar data interpolation on surfaces. Numerische Mathematik, 102 (3). pp. 383-411. ISSN 0029-599X

Cohen, D. and Jahnke, T. and Lorenz, K. and Lubich, Ch. (2006) Numerical Integrators for Highly Oscillatory Hamiltonian Systems: A Review. In: Analysis, Modeling and Simulation of Multiscale Problems.

Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128.

Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Schütte, Ch. (2006) Graph Algorithms for Dynamical Systems. In: Analysis, Modeling and Simulation of Multiscale Problems.

Deuflhard, P. and Ertel, S. and Kornhuber, R. and Krause, R. and Sander, O. (2006) Patient-specific simulation of dynamic stress distribution in the human knee. Journal of Biomechanics, 39 . p. 47. ISSN 0021-9290

Gebauer, S. and Kornhuber, R. and Yserentant, H. (2006) Hierarchical decomposition of domains with fractures. Mathematics of Computation, 75 (253). pp. 73-90. ISSN 00255718

Horenko, I. and Dittmer, E. and Fischer, A. and Schütte, Ch. (2006) Automated Model Reduction for Complex Systems exhibiting Metastability. Mult. Mod. Sim., 5 (3). pp. 802-827.

Horenko, I. and Hartmann, C. (2006) Blind Model Reduction for High-Dimensional Time-Dependent Data. Technical Report. Freie Universität Berlin. (Unpublished)

Horenko, I. and Schmidt-Ehrenberg, J. and Schütte, Ch. (2006) Set-Oriented Dimension Reduction: Localizing Principal Component Analysis via Hidden Markov Models. In: Computational Life Sciences II.

Kornhuber, R. and Krause, R. (2006) Robust multigrid methods for vector-valued Allen-Cahn equations with logarithmic free energy. Computing and Visualization in Science, 9 (2). pp. 103-116. ISSN 1432-9360

Krause, R. and Sander, O. (2006) Automatic construction of boundary parametrizations for geometric multigrid solvers. Computing and Visualization in Science, 9 (1). pp. 11-22. ISSN 1432-9360

Lorenz, S. (2006) The model-data-overlap: A new approach to parameter estimation, model validation, selection and discrimination. PhD thesis, Free University of Berlin.

Meerbach, E. and Dittmer, E. and Horenko, I. and Schütte, Ch. (2006) Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States. In: Computer Simulations in Condensed Matter: Systems: From Materials to Chemical Biology. Volume I.

Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2006) Illustration of Transition Path Theory on a Collection of Simple Examples. J. Chem. Phys., 125 (8). 084110.

Sander, O. (2006) A fast solver for finite deformation contact problems. Preprint A-06-02 . (Unpublished)

Telgmann, R. and von Kleist, M. and Huisinga, W. (2006) Software Supported Modelling in Pharmacokinetics. In: Computational Life Sciences II.

Walter, J. (2006) Averaging for Diffusive Fast-Slow Systems with Metastability in the Fast Variable. PhD thesis, Free University of Berlin.

Walter, J. and Schütte, Ch. (2006) Conditional Averaging for Diffusive Fast-Slow Systems: A Sketch for Derivation. In: Analysis, Modeling and Simulation of Multiscale Problems.

Weiße, A. Y. and Horenko, I. and Huisinga, W. (2006) Adaptive Approach for Modelling Variability in Pharmacokinetics. In: Computational Life Sciences II.

2005

Kornhuber, R. and Hoppe, R. and Périaux, J. and Pironneau, O. and Widlund, O. and Xu, J., eds. (2005) Domain decomposition methods in science and engineering. Lecture Notes in Computational Science and Engineering, 40 . Springer, Berlin. ISBN 978-3-540-22523-2

Chipot, C. and Elber, R. and Laaksonen, A. and Leimkuhler, B. and Mark, A. and Schlick, T. and Schütte, Ch. and Skeel, R., eds. (2005) New Algorithms for Macromolecular Simulation. Lecture Notes in Computational Science and Engineering, 49 . Springer.

Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309.

Antony, J. and von Helden, G. and Meijer, G. and Schmidt, B. (2005) Anharmonic Midinfrared Vibrational Spectra of Benzoic Acid Monomer and Dimer. J. Chem. Phys., 123 (1). 014305.

Dellnitz, M. and Neumann, M. and Schütte, Ch. (2005) Special Issue on Matrices and Mathematical Biology. Lin. Alg. Appl., 398 . pp. 1-245.

Gonzalez, L. and Manz, J. and Schmidt, B. and Shibl, M. F. (2005) Optical resolution of oriented enantiomers via photodissociation: Quantum simulations for H2POSD. Phys. Chem. Chem. Phys., 7 (24). pp. 4096-4101.

Hartmann, C. and Schütte, Ch. (2005) A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables. Z. Angew. Math. Mech., 85 (10). pp. 700-710.

Hartmann, C. and Schütte, Ch. (2005) A Geometric Approach to Constrained Molecular Dynamics and Free Energy. Comm. Math. Sci., 3 (1). pp. 1-20.

Horenko, I. and Dittmer, E. and Schütte, Ch. (2005) Reduced Stochastic Models for Complex Molecular Systems. Comp. Vis. Sci., 9 (2). pp. 89-102.

Horenko, I. and Lorenz, S. and Schütte, Ch. and Huisinga, W. (2005) Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics. J. Comp. Chem., 26 (9). pp. 941-948.

Huisinga, W. and Schmidt, Bernd (2005) Metastability and Dominant Eigenvalues of Transfer Operators. In: New Algorithms for Macromolecular Simulation.

Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Aligning and Orienting Molecules Trapped in Octahedral Crystal Fields. Phys. Rev. A, 72 (5). 053415.

Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Intense-Field Alignment of Molecules Confined in Octahedral Field. Phys. Rev. Lett., 94 (12). p. 123003.

Krause, R. and Sander, O. (2005) Fast solving of contact problems on complicated geometries. In: Domain Decomposition Methods in Science and Engineering XIII. Lecture Notes in Computational Science and Engineering, 40 . Springer, Berlin, pp. 495-502. ISBN 978-3-540-22523-2

Lasser, C. and Teufel, St. (2005) Propagation through conical crossings: An asymptotic semigroup. Comm. Pure Appl. Math., 58 (9). pp. 1188-1230.

Lorenz, K. and Jahnke, T. and Lubich, Ch. (2005) Adiabatic Integrators for Highly Oscillatory Second-Order Linear Differential Equations with Time-Varying Eigendecomposition. BIT Num. Math., 45 (1). pp. 91-115.

Meerbach, E. and Schütte, Ch. and Fischer, A. (2005) Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 398 . pp. 141-160.

Rack, A. (2005) Prediction of Post-translational Modifications of Proteins from 2-DE/MS Data. Masters thesis, Freie Universität Berlin.

Schütte, Ch. and Forster, R. and Meerbach, E. and Fischer, A. (2005) Uncoupling-Coupling Techniques for Metastable Dynamical Systems. In: Domain Decomposition Methods in Science and Engineering.

2004

Conrad, T. O. F. (2004) Metabolic Pathways. Other thesis, Monash University Melbourne.

Conrad, T. O. F. (2004) New Approaches for Visualizing and Analyzing Metabolic Pathways. Proceedings of the Second Australian Undergraduate Students’ Computing Conference .

Deuflhard, P. and Schütte, Ch. (2004) Molecular Conformation Dynamics and Computational Drug Design. In: Applied Mathematics Entering the 21st Century.

Fujimura, Y. and Gonzalez, L. and Kröner, D. and Manz, J. and Mehdaoui, I. and Schmidt, B. (2004) Quantum Ignition of Intramolecular Rotation by Means of IR+UV Laser Pulses. Chem. Phys. Lett., 386 (4-6). pp. 248-253.

Horenko, I. and Weiser, M. and Schmidt, B. and Schütte, Ch. (2004) Fully Adaptive Propagation of the Quantum-Classical Liouville Equation. J. Chem. Phys., 120 (19). pp. 8913-8923.

Huisinga, W. and Meyn, S. and Schütte, Ch. (2004) Phase Transitions and Metastability in Markovian and Molecular Systems. Ann. Appl. Prob., 14 (1). pp. 419-458.

Jahnke, T. (2004) A Long-Time-Step Method for Quantum-Classical Molecular Dynamics. SIAM J. Sci. Comp., 25 (6). pp. 2145-2164.

Kiljunen, T. and Bargheer, M. and Gühr, M. and Schwentner, N. and Schmidt, B. (2004) Photodynamics and Ground State Librational States of ClF Molecule in solid Ar. Comparison of experiment and theory. Phys. Chem. Chem. Phys., 6 (11). pp. 2932-2939.

Korolkov, M. V. and Schmidt, B. (2004) Quantum Molecular Dynamics Driven by Short and Intense Light Pulses: Towards the Limits of the Floquet Picture. Comp. Phys. Comm., 161 (1-2). pp. 1-17.

Preis, R. and Dellnitz, M. and Hessel, M. and Schütte, Ch. and Meerbach, E. (2004) Dominant Paths Between Almost Invariant Sets of Dynamical Systems. preprint .

Ronen, S. and Nachtigallova, D. and Schmidt, B. and Jungwirth, P. (2004) Non-Adiabatic Chemical Reaction Triggered by Electron Photodetachment: An ab initio Quantum Dynamical Study. Phys. Rev. Lett., 93 (4). 048301.

Schütte, Ch. and Walter, J. and Hartmann, C. and Huisinga, W. (2004) An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations. Multiscale Model. Simul., 2 (3). pp. 501-526.

Walter, J. and Schütte, Ch. and Pavliotis, G. A. and Stuart, A. (2004) Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited. preprint .

2003

Berninger, H. and Werner, Dirk (2003) Lipschitz spaces and M-ideals. Extracta Mathematicae, 18 (1). pp. 33-56. ISSN 0213-8743

Conrad, T. O. F. (2003) Berechnung von freien Energie Flächen am Beispiel des Alanin-Dipeptides. Other thesis, Freie Universität Berlin.

Fermanian Kammerer, C. and Lasser, C. (2003) Wigner measures and codimension two crossings. J. Math. Phys., 44 (2). pp. 507-557.

Fischer, A. (2003) An Uncoupling-Coupling Method for Markov Chain Monte Carlo Simulations with an Application to Biomolecules. PhD thesis, Free University of Berlin.

Horenko, I. and Weiser, M. (2003) Adaptive Integration of Molecular Dynamics. J. Comp. Chem., 24 (15). pp. 1921-1929.

Huisinga, W. and Schütte, Ch. and Stuart, A. M. (2003) Extracting Macroscopic Stochastic Dynamics: Model Problems. Comm. Pure Appl. Math., 56 (2). pp. 234-269.

Kornhuber, R. and Krause, R. (2003) On multigrid methods for vector-valued Allen-Cahn equations. In: Proceedings of the fourteenth international conference on domain decomposition methods. National Autonomous University of Mexico (UNAM), Mexico City, Cocoyoc, Mexico, pp. 307-314. ISBN 970-32-0859-2

Krah, A. and Schmidt, F. and Becher, D. and Schmid, M. and Albrecht, D. and Rack, A. and Büttner, K. and Jungblut, P. (2003) Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis. Molecular & Cellular Proteomics, 2 (12). pp. 1271-1283.

Sander, O. and Caselles, V. and Bertalmio, M. (2003) Axiomatic scalar data interpolation on manifolds. In: International Conference on Image Processing (ICIP) 2003. Proceedings. IEEE, Barcelona, Spain, pp. 681-684. ISBN 0-7803-7750-8

Schütte, Ch. and Huisinga, W. (2003) Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics. In: Special Volume: Computational Chemistry.

Schütte, Ch. and Huisinga, W. and Meyn, S. (2003) Metastability of Diffusion Processes. In: Nonlinear Stochastic Dynamics.

Wohlmuth, B. and Krause, R. (2003) Monotone methods on non-matching grids for non-linear contact problems. SIAM J. Sci. Comput., 25 (1). pp. 324-347. ISSN 1064-8275

2002

Berghof, V. and Martins, M. and Schmidt, B. and Schwentner, N. (2002) Vibrational Overtones and Rotational Structures of HCl in Rare Gas Matrices. J. Chem. Phys., 116 (21). pp. 9364-9373.

Fischer, A. and Schütte, Ch. and Deuflhard, P. and Cordes, F. (2002) Hierarchical Uncoupling-Coupling of Metastable Conformations. In: Computational Methods for Macromolecules: Challenges and Applications.

Gebauer, S. and Neunhäuserer, L. and Kornhuber, R. and Ochs, S. and Hinkelmann, R. and Helmig, R. (2002) Equidimensional modelling of flow and transport processes in fractured porous systems I. In: Computational Methods in Water Resources. Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV). Computational Methods in Water Resources (CMWR XIV), Delft, pp. 335-342. ISBN 978-0-444-50975-8

Horenko, I. and Salzmann, Ch. and Schmidt, B. and Schütte, Ch. (2002) Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets. J. Chem. Phys., 117 (24). pp. 11075-11088.

Horenko, I. and Schmidt, B. and Schütte, Ch. (2002) Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions. J. Chem. Phys., 117 (10). pp. 4643-4650.

Kornhuber, R. (2002) On constrained Newton linearization and multigrid for variational inequalities. Numerische Mathematik, 91 (4). pp. 699-721. ISSN 0029-599X

Korolkov, M. V. and Schmidt, B. (2002) Spin-Orbit Induced Association under Ultrafast Laser Pulse Control. Chem. Phys. Lett., 361 (5-6). pp. 432-438.

Krause, R. and Wohlmuth, B. (2002) A Dirichlet-Neumann type algorithm for contact problems with friction. Computing and Visualization in Science, 5 (3). pp. 139-148. ISSN 1432-9360

Manz, J. and Proppe, B. and Schmidt, B. (2002) Time-Resolved Dual Fluorescence of 1-Phenylpyrrole in Acetonitrile: Molecular Dynamics Symulations of Solvent Response to Twisted Intramolecular Charge Transfer. Phys. Chem. Chem. Phys., 4 (10). pp. 1876-1881.

Neunhäuserer, L. and Gebauer, S. and Ochs, S. and Hinkelmann, R. and Kornhuber, R. and Helmig, R. (2002) Equidimensional modelling of flow and transport processes in fractured porous systems II. In: Computational Methods in Water Resources. Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV). Computational Methods in Water Resources (CMWR XIV), Delft, pp. 343-350. ISBN 978-0-444-50975-8

Ochs, S. and Hinkelmann, R. and Neunhäuserer, L. and Süß, M. and Helmig, R. and Gebauer, S. and Kornhuber, R. (2002) Adaptive methods for the equidimensional modelling of flow and transport processes in fractured aquifers. In: 5th International Conference on Hydroscience and Engineering, ICHE2002, Advances in Hydro-Science and -Engineering., Sept. 17-21, 2002, Warschau.

Roeselova, M. and Mucha, M. and Schmidt, B. and Jungwirth, P. (2002) Quantum dynamics and spectroscopy of photodetachment in Cl-...H2O and Cl-...D2O complexes. J. Phys. Chem. A, 106 (51). pp. 12229-12241.

2001

Chaban, G. and Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2001) Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ultrashort Laser Pulses. J. Phys. Chem. A, 105 (12). pp. 2770-2782.

Erdmann, B. and Kober, C. and Lang, J. and Deuflhard, P. and Zeilhofer, H.-F. and Sader, R. (2001) Efficient and reliable finite element methods for simulation of the human mandible. In: Proceedings of Medicine Meets Mathematics. Kloster Banz/Staffelstein. Report ZIB 01-14, 2001. (Submitted)

Hartmann, C. and Schmidt, H.-J. (2001) A WKB approximation for the nonlinear Schrödinger-Newton equations. Technical Report. Universität Osnabrück. (Unpublished)

Horenko, I. and Schmidt, B. and Schütte, Ch. (2001) A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation. J. Chem. Phys., 115 (13). pp. 5733-5743.

Huisinga, W. (2001) Metastability of Markovian Systems A transfer operator based approach in application to molecular dynamics. PhD thesis, Free University of Berlin.

Kober, C. and Müller-Hannemann, M. (2001) A case study in hexahedral mesh generation: Simulation of the human mandible. Engineering with Computers, 17 (3). pp. 249-260. ISSN 0177-0667

Kober, C. and Sader, R. and Zeilhofer, H.-F. and Prohaska, S. and Zachow, S. and Deuflhard, P. (2001) Anisotrope Materialmodellierung für den menschlichen Unterkiefer. In: Tagungsband des Workshops "Die Methode der Finiten Elemente in der Biomedizin, Biomechanik und angrenzenden Gebieten". Universitätsklinikum/Universitätsrechenzentrum, Ulm. ISBN 978-3980618342

Kornhuber, R. (2001) Nonlinear multigrid techniques. In: Theory and Numerics of Differential Equations. Durham 2000. Universitext . Springer Berlin Heidelberg, pp. 179-229. ISBN 978-3-642-07533-9

Kornhuber, R. and Krause, R. (2001) Adaptive multigrid methods for Signorini's problem in linear elasticity. Computing and Visualization in Science, 4 (1). pp. 9-20. ISSN 1432-9360

Krause, R. and Wohlmuth, B. (2001) Domain decomposition methods on nonmatching grids and some applications to linear elasticity problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 81 (Suppl.). pp. 21-24. ISSN 0044-2267

Müller-Hannemann, M. and Kober, C. and Sader, R. and Zeilhofer, H.-F. (2001) Anisotropic validation of hexahedral meshes for composite materials in biomechanics. In: Proceedings of the 10th International Meshing Roundtable. International Meshing Roundtable, Newport Beach, CA, pp. 249-260.

Schütte, Ch. and Huisinga, W. and Deuflhard, P. (2001) Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems. In: Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems.

Slavicek, P. and Roeselova, M. and Jungwirth, P. and Schmidt, B. (2001) Preference of Cluster Isomers as a Result of Quantum Delocalization: Potential Energy Surfaces and Intermolecular Vibrational States of Ne...HBr, Ne...HI, and HI(Ar)n (n=1-6). J. Chem. Phys., 114 (4). pp. 1539-1548.

Wohlmuth, B. and Krause, R. (2001) A multigrid method based on the unconstrained product space for Mortar finite element discretizations. SIAM Journal on Numerical Analysis, 39 (1). pp. 192-213. ISSN 0036-1429

2000

Deuflhard, P. and Huisinga, W. and Fischer, A. and Schütte, Ch. (2000) Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 315 (1-3). pp. 39-59.

Fischer, A. (2000) An Uncoupling-Coupling Technique for Markov Chain Monte Carlo Methods. preprint .

Galliat, T. and Huisinga, W. and Deuflhard, P. (2000) Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification. In: Neural Computation.

Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2000) A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulation for F2 in Ar. Chem. Phys. Lett., 327 (1-2). pp. 76-84.

Huisinga, W. (2000) The Essential Spectral Radius and Asymptotic Properties of Transfer Operators. preprint .

Kober, C. (2000) Composite material with shape memory alloy fibers. In: Communications of the Bexbach Colloquium on Science 2000. Shaker, Aachen. ISBN 978-3-8322-1517-0

Kober, C. and Sader, R. and Thiele, H. and Bauer, H.-J. and Zeilhofer, H.-F. and Hoffmann, K.-H. (2000) FEM simulations versus biomechnical experiments concerning the human mandible: a comparision of the results of a frontal and a molar biting study. Preprint A-21-2000 . (Unpublished)

Krause, R. and Wohlmuth, B. (2000) Multigrid methods for Mortar finite elements. In: Multigrid Methods VI. Proceedings of the Sixth European Multigrid Conference Held in Gent, Belgium, September 27–30. Springer Berlin Heidelberg, pp. 136-142. ISBN 978-3-540-67157-2

Krause, R. and Wohlmuth, B. (2000) Nonconforming decomposition methods: Techniques for linear elasticity. East-West Journal of Numerical Mathematics, 8 (3). pp. 177-206. ISSN 1569-3953; 0928-0200

Neunhäuserer, L. and Gebauer, S. and Hinkelmann, R. and Kornhuber, R. and Helmig, R. (2000) Mehrgittermethoden und adaptive Diskretisierungsverfahren zur Simulation von Strömungs- und Transportprozessen in Kluftaquiferen. In: 3. Workshop Kluft-Aquifere "Gekoppelte Prozesse in Geosystemen". Institut für Strömungsmechanik und Elektronisches Rechnen im Bauwesen, Hannover, pp. 241-255.

Schmidt, B. and Zdanska, P. (2000) Solution of the Time-Dependent Schrödinger Equation for Highly Symmetric Potentials. Comp. Phys. Comm., 127 (2-3). pp. 290-308.

Schütte, Ch. and Cordes, F. (2000) On Dynamical Transitions between Conformational Ensembles. In: Molecular Dynamics on Parallel Computers.

Schütte, Ch. and Huisinga, W. (2000) Biomolecular Conformations as Metastable Sets of Markov Chains. In: Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA.

Schütte, Ch. and Huisinga, W. (2000) On Conformational Dynamics induced by Langevin Processes. In: Equadiff 99.

1999

Backhaus, P. and Schmidt, B. and Dantus, M. (1999) Control of Photoassociation Yield: A Quantum Dynamical Study of the Mercury System to Explore the Role of Pulse Duration from Nanoseconds to Femtoseconds. Chem. Phys. Lett., 306 (1-2). pp. 18-24.

Bornemann, F. A. and Schütte, Ch. (1999) Adaptive Accuracy Control for Car-Parrinello Simulations. Num. Math., 83 (2). pp. 179-186.

Bornemann, F. A. and Schütte, Ch. (1999) On the Singular Limit of the Quantum-Classical Molecular Dynamics Model. J. Appl. Math., 59 (4). pp. 1208-1224.

Deuflhard, P. and Dellnitz, M. and Junge, O. and Schütte, Ch. (1999) Computation of Essential Molecular Dynamics by Subdivision Techniques. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Fischer, A. and Cordes, F. and Schütte, Ch. (1999) Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA. Comp. Phys. Comm., 121 . pp. 37-39.

Huisinga, W. and Best, Ch. and Roitzsch, R. and Schütte, Ch. and Cordes, F. (1999) From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J. Comp. Chem., 20 (16). pp. 1760-1774.

Huisinga, W. and Pesce, L. and Kosloff, R. and Saalfrank, P. (1999) Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation. J. Chem. Phys., 110 (12). pp. 5538-5547.

Kornhuber, R. (1999) Monotone iterations for elliptic variational inequalities. In: Free boundary problems: theory and applications. Research notes in mathematics (409). Chapman & Hall/CRC, Boca Raton, London, New York, Washington, D.C., pp. 335-343. ISBN 1-58488-018-X

Nettesheim, P. and Reich, S. (1999) Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Nettesheim, P. and Schütte, Ch. (1999) Numerical Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Schütte, Ch. (1999) Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules. preprint .

Schütte, Ch. (1999) Partial Wigner transforms and the quantum-classical Liouville equation. Other thesis, UNSPECIFIED.

Schütte, Ch. and Bornemann, F. A. (1999) Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Schütte, Ch. and Fischer, A. and Huisinga, W. and Deuflhard, P. (1999) A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comp. Phys, 151 (1). pp. 146-168.

Schütte, Ch. and Nettesheim, P. (1999) Nonadiabatic Effects in Quantum-Classical Molecular Dynamics. In: Scientific Computing in Chemical Engineering II.

1998

Bornemann, F. A. and Schütte, Ch. (1998) A mathematical investigation of the Car-Parrinello Method. Num. Math., 78 (3). pp. 359-376.

Fischer, A. and Cordes, F. and Schütte, Ch. (1998) Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA. J. Comp. Chem., 19 (15). pp. 1689-1697.

Kornhuber, R. (1998) On robust multigrid methods for non-smooth variational problems. In: Multigrid methods 5: Proceedings of the Fifth European Multigrid Conference held in Stuttgart, Germany, October 1.4, 1996. Lecture Notes in Computational Science and Engineering (3). Springer Berlin Heidelberg, pp. 173-188. ISBN 978-3-540-63133-0

Nettesheim, P. (1998) Second Order Transitions in Quantum-Classical Molecular Dynamics. preprint .

1997

Bornemann, F. A. and Schütte, Ch. (1997) Homogenization of Hamiltonian Systems with a Strong Constraining Potential. Physica D, 102 (1-2). pp. 57-77.

Kornhuber, R. (1997) Adaptive monotone multigrid methods for nonlinear variational problems. Advances in Numerical Mathematics . Vieweg+Teubner Verlag, Stuttgart. ISBN 3519027224

Kornhuber, R. (1997) Adaptive monotone multigrid methods for some non-smooth optimization problems. In: Domain decomposition methods in science and engineering: 8th international conference, Bejing, P.R. China. John Wiley & Sons, pp. 177-191. ISBN 047196560X

Schütte, Ch. and Bornemann, F. A. (1997) Homogenization Approach to Smoothed Molecular Dynamics. Nonlinear Analysis, 30 (3). pp. 1805-1814.

1996

Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1996) A posteriori error estimates for elliptic problems in two and three space dimensions. SIAM Journal on Numerical Analysis, 33 (3). pp. 1188-1204. ISSN 0036-1429

Bornemann, F. A. and Nettesheim, P. and Schütte, Ch. (1996) Quantum-classical molecular dynamics as an approximation to full quantum dynamics. J. Chem. Phys., 105 (3). pp. 1074-1083.

Kornhuber, R. (1996) Monotone multigrid methods for elliptic variational inequalities II. Numerische Mathematik, 72 (4). pp. 481-499. ISSN 0029-599X

Kornhuber, R. (1996) A posteriori error estimates for elliptic variational inequalities. Computers & Mathematics with Applications, 31 (8). pp. 49-60. ISSN 0898-1221

Nettesheim, P. and Bornemann, F. A. and Schmidt, B. and Schütte, Ch. (1996) An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics. Chem. Phys. Lett., 256 (6). pp. 581-588.

Nettesheim, P. and Huisinga, W. and Schütte, Ch. (1996) Chebyshev-Approximation for Wavepacket-Dynamics: better than expected. preprint .

1995

Schütte, Ch. (1995) Smoothed Molecular Dynamics for Thermally Embedded Systems. preprint . (Unpublished)

Schütte, Ch. and Dinand, M. (1995) Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers. J. Lightw. Techn., 13 (1). pp. 14-23.

Schütte, Ch. and Zumbusch, M. D. G and Brinkmann, R. (1995) Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments. preprint .

1994

Erdmann, B. and Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel-methods for obstacle problems in three space dimensions. In: Adaptive Methods - Algorithms, Theory and Applications. Notes on Numerical Fluid Mechanics (NNFM), 46 . Vieweg+Teubner Verlag, pp. 120-141. ISBN 978-3-528-07646-7

Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel methods for obstacle problems. SIAM Journal on Numerical Analysis, 31 (2). pp. 301-323. ISSN 0036-1429

Kornhuber, R. (1994) Monotone multigrid methods for elliptic variational inequalities I. Numerische Mathematik, 69 (2). pp. 167-184. ISSN 0029-599X

Kornhuber, R. and Yserentant, H. (1994) Multilevel methods for elliptic problems on domains not resolved by the coarse grid. In: Domain Decomposition Methods in Scientific and Engineering Computing. Contemporary Mathematics, 180 . American Mathematical Society, Providence, Rhode Island, pp. 49-60. ISBN 0-8218-5171-3

Manz, J. and Paramonov, G. K. and Polasek, M. and Schütte, Ch. (1994) Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D. Isr. J. Chem., 34 (1). pp. 115-125.

1993

Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1993) Adaptive multilevel methods in three space dimensions. International Journal for Numerical Methods in Engineering, 36 (18). pp. 3187-3203. ISSN 1097-0207

Erdmann, B. and Frei, M. and Hoppe, R. H. W. and Kornhuber, R. and Wiest, U. (1993) Adaptive finite element methods for variational inequalities. East-West Journal of Numerical Mathematics, 1 . pp. 165-197. ISSN 1569-3953; 0928-0200

Kornhuber, R. and Roitzsch, R. (1993) Self-adaptive finite-element simulation of bipolar, strongly reverse-biased pn-junctions. International Journal for Numerical Methods in Biomedical Engineering, 9 (3). pp. 243-250. ISSN 2040-7947

Kornhuber, R. and Wittum, G. (1993) Discretization and preconditioning of convection diffusion equations. In: Incomplete Decomposition (ILU) - Algorithms, Theory, and Applications. Notes on Numerical Fluid Mechanics (41). Springer Vieweg, pp. 67-77. ISBN 978-3-528-07641-2

Schütte, Ch. (1993) A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation. Impact of Computing in Sci. Eng., 5 (3). pp. 176-200.

1992

Schütte, Ch. and Wulkow, M. (1992) Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. preprint .

1991

Kornhuber, R. and Roitzsch, R. (1991) Self adaptive computation of the breakdown voltage of planar pn-junctions with multistep field plates. In: Proc. 4th International Conference on Simulation of Semiconductor Devices and Processes. Hartung-Gorre Verlag, Zürich, pp. 535-543. ISBN 3-89191-476-8

1990

Hoppe, R. H. W. and Kornhuber, R. (1990) Multi-grid solution of two coupled Stefan equations arising in induction heating of large steel slabs. International Journal for Numerical Methods in Engineering, 30 (4). pp. 779-801. ISSN 1097-0207

Kornhuber, R. and Roitzsch, R. (1990) On adaptive grid refinement in the presence of internal or boundary layers. IMPACT of Computing in Science and Engineering, 2 (1). pp. 40-72. ISSN 0899-8248

Roitzsch, R. and Kornhuber, R. (1990) BOXES - a program to generate triangulations from a rectangular domain description. ZIB-Report, TR-90- . ISSN 1438-0064

1989

Hoppe, R. H. W. and Kornhuber, R. (1989) Numerical simulation of induction heating processes by multi-grid techniques. In: Numerical methods in Thermal Problems. Pineridge Press, Swansea, pp. 1142-1152.

Kornhuber, R. and Roitzsch, R. (1989) Adaptive Finite-Element-Methoden für konvektionsdominierte Randwertprobleme bei partiellen Differentialgleichungen. ZIB-Report . ISSN 1438-0064

1988

Hoppe, R. H. W. and Kornhuber, R. (1988) Multi-grid solution of the two-phase Stefan problem. In: Multigrid Methods: Theory, Applications and Supercomputing. Lecture Notes in Pure and Applied Mathematics (110). Marcel Dekker Inc., pp. 267-297. ISBN 0824779797, 978-0824779795

Kornhuber, R. (1988) Convergent extensions of grid-functions. Mathematische Nachrichten, 139 (1). pp. 63-75. ISSN 1522-2616

Kornhuber, R. (1988) Local change of coordinates for grid-functions on regions with curved boundary. Mathematische Nachrichten, 139 (1). pp. 45-61. ISSN 1522-2616

This list was generated on Sun Sep 24 09:02:50 2017 CEST.