This page is dedicated to the scientific publications I've taken a part in, please refer to Talks and Articles and Stuff for Computer Science-oriented stuff (mostly German, though)

Clojure - Grundlagen, Concurrent Programming, Java

Stefan Kamphausen, Tim Oliver Kaiser.


Thrombin inhibitors identified by computer-assisted multiparameter design

Daniel Riester, Frank Wirsching, Gabriela Salinas, Martina Keller, Michael Gebinoga, Stefan Kamphausen, Christian Merkwirth, Ruediger Goetz, Martin Wiesenfeldt, Jörg Stürzebecher, Wolfram Bode, Rainer Friedrich, Marcel Thürk, and Andreas Schwienhorst

Proceedings of the National Academy of Sciences of the United States of America (PNAS) 2005 102: 8597-8602; published online before print June 3 2005, 10.1073/pnas.0501983102

PNAS Issue online (needs subscription)

Here, we present a series of thrombin inhibitors that were generated by using powerful computer-assisted multiparameter optimization process. The process was organized in design cycles, starting with a set of randomly chosen molecules. Each cycle combined combinatorial synthesis, multiparameter characterization of compounds in a variety of bioassays, and algorithmic processing of the data to devise a set of compounds to be synthesized in the next cycle. The identified lead compounds exhibited thrombin inhibitory constants in the lower nanomolar range. They are by far the most selective synthetic thrombin inhibitors, with selectivities of >100,000-fold toward other proteases such as Factor Xa, Factor XIIa, urokinase, plasmin, and Plasma kallikrein. Furthermore, these compounds exhibit a favorable profile, comprising nontoxicity, high metabolic stability, low serum protein binding, good solubility, high anticoagulant activity, and a slow and exclusively renal elimination from the circulation in a rat model. Finally, x-ray crystallographic analysis of a thrombin?inhibitor complex revealed a binding mode with a neutral moiety in the S1 pocket of thrombin.

Genetic algorithm for the design of molecules with desired properties

Stefan Kamphausen, Nils Höltge, Frank Wirsching, Corinna Morys-Wortmann, Daniel Riester, Ruediger Goetz, Marcel Thürk and Andreas Schwienhorst

Journal of Computer-Aided Molecular Design, 16, 551-567, 2002.

Please not that I am only responsible for the multi-parent crossover algorithm and the numerical experiments using the RNA folding software.
The design of molecules with desired properties is still a challenge because of the largely unpredictable end results. Computational methods can be used to assist and speed up this process. In particular, genetic algorithms have proved to be powerful tools with a wide range of applications, e.g. in the field of drug development. Here, we propose a new genetic algorithm that has been tailored to meet the demands of de novo drug design, i.e. efficient optimization based on small training sets that are analyzed in only a small number of design cycles. The efficiency of the design algorithm was demonstrated in the context of several different applications. First, RNA molecules were optimized with respect to folding energy. Second, a spinglass was optimized as a model system for the optimization of multiletter alphabet biopolymers such as peptides. Finally, the feasibility of the computer-assisted molecular design approach was demonstrated for the de novo construction of peptidic thrombin inhibitors using an iterative process of 4 design cycles of computer-guided optimization. Synthesis and experimental fitness determination of only 600 different compounds from a virtual library of more than 10^{17} molecules was necessary to achieve this goal.

Dynamics of delay-coupled spherical bubbles

R. Mettin, S. Luther, S. Kamphausen, and W. Lauterborn

Drittes Physikalisches Institut, Universität Göttingen, Bürgerstraße 42-44, D-37073 Göttingen, Germany

(s. auch Robert Mettin: Publications)

The behavior of mutually coupled cavitation bubbles might change considerably when a finite speed of sound propagation in the liquid is taken into account. This holds for the radial oscillations of the bubbles as well as for the interaction (Bjerknes) forces between them. Starting from linear analysis of the equations of motion, nonlinear bubble dynamics is investigated numerically. Some results are reported for illustration of effects that might have significant impact on the modeling of cavitation structures in certain parameter regimes.
to appear in
W. Lauterborn and T. Kurz (eds.): Proceedings of the 15th International Symposium on Nonlinear Acoustics Göttingen, Germany 1-4 Sept. 1999