1. M. Weber, S. Kube, L. Walter, P. Deuflhard: Stable Computation of Probability Densities of Metastable Dynamical Systems. SIAM J. Multiscale Model. Simul. 6(2), pp. 396-416 (2007).

  2. P. Deuflhard, Ch. Schütte: Molecular Conformation Dynamics and Computational Drug Design. In: J.M. Hill, R. Moore (eds), Applied Mathematics Entering the 21st Century, Invited Talks from the ICIAM 2003 Congress, Sydney, Australia, pp. 91-119 (2004).

  3. P. Deuflhard, M. Weber: Robust Perron Cluster Analysis in Conformation Dynamics. In: M. Dellnitz, S. Kirkland, M. Neumann and C. Schütte (eds.), Linear Algebra and Its Applications: Special Issue on Matrices and Mathematical Biology, Vol. 398C, pp. 161-184 (2004)

  4. P. Deuflhard: From Molecular Dynamics to Conformational Dynamics in Drug Design. Konrad-Zuse-Zentrum Berlin. ZIB-Report 02-20 (April 2002). Appeared in: M. Kirkilionis, S. Krömker, R. Rannacher, F. Toni (eds.). Trends in Nonlinear Analysis, Springer, pp. 269-288 (2003).

  5. P. Deuflhard, F. Bornemann: Scientific Computing with Ordinary Differential Equations. Texts in Applied Mathematics 42, Springer (2002).

  6. P. Deuflhard, F. Bornemann: Numerische Mathematik II. Gewöhnliche Differentialgleichungen. 2. vollständig überarbeitete und erweiterte Auflage. de Gruyter: Berlin, New York (2002).

  7. A. Fischer, Ch. Schütte, P. Deuflhard, F. Cordes: Hierarchical Uncoupling-Coupling of Metastable Conformations. In: T.Schlick and H.H.Gan (eds.), Computational Methods for Macromolecules: Challenges and Applications. Proceedings of the 3rd International Workshop on Methods for Macromolecular Modeling, New York, 2000, Lecture Notes in Computational Science and Engineering (LNCSE), Vol. 24, Springer Verlag, (2002).

  8. T. Galliat, P. Deuflhard, R. Roitzsch, F. Cordes: Automatic Identification of Metastable Conformations via Self-Organized Neural Networks. In: T.Schlick and H.H.Gan (eds.), Computational Methods for Macromolecules: Challenges and Applications. Proceedings of the 3rd International Workshop on Methods for Macromolecular Modeling, New York, 2000, Lecture Notes in Computational Science and Engineering (LNCSE), Vol. 24, Springer Verlag, (2002).

  9. T. Galliat, W. Huisinga, P. Deuflhard: Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification. Konrad-Zuse-Zentrum Berlin, Preprint SC 99-38.

  10. P. Deuflhard: Differential Equations in Technology and Medicine. Computational Concepts, Adaptive Algorithms, and Virtual Labs. Computational Mathematics Driven by Industrial Applications. Lecture Notes in Mathematics 1739, Springer-Verlag, pp. 69-125 (2000).

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

  12. P. Deuflhard, Ch. Schütte, F. Cordes, L. Müller-Kurth: Konformationsdynamik. Mathematischer Entwurf hochspezifischer Biomoleküle. In: D. Hömberg (ed.), 8. Veranstaltungsreihe Forschungspolitische Dialoge in Berlin: Angewandte Mathematik - die verborgene Schlüsseltechnologie, 30. April 1999, Konrad-Zuse-Zentrum Berlin, pp. 30-34 (1999).

  13. Ch. Schütte, W. Huisinga, P. Deuflhard: Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems. Konrad-Zuse-Zentrum Berlin, Preprint SC 99-36.

  14. Ch. Schütte, A. Fischer, W. Huisinga, P. Deuflhard: A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comput. Phys., Special Issue Comp. Biophysics,Academic Press, Vol. 151, pp. 146--169 (1999).

  15. Ch. Schütte, A. Fischer, W. Huisinga, P. Deuflhard: A Hybird Monte-Carlo Method for Essential Molecular Dynamics. Konrad-Zuse-Zentrum Berlin, Preprint SC 98-04 (1998)

  16. P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S.Reich, B. Skeel (eds): Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, Vol. 4, Springer-Verlag (1998).

  17. P. Deuflhard, M. Dellnitz, O. Junge, Ch. Schütte: Computation of Essential Molecular Dynamics by Subdivision Techniques. In: P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel (eds.), Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, Vol. 4, Springer-Verlag, pp. 98-115 (1998).