Thomas Hinze

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We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because(More)
Systems biology is the ever-growing field of integrating molecular knowledge about biological organisms into an understanding at the systems level. For this endeavour, automatic network reconstruction tools are urgently needed. In the present contribution, we show how the applicability of evolutionary algorithms to systems biology can be improved by a(More)
Modelling and simulation of biological reaction networks is an essential task in systems biology aiming at formalisation, understanding , and prediction of processes in living organisms. Currently, a variety of modelling approaches for specific purposes coexists. P systems form such an approach which owing to its algebraic nature opens growing fields of(More)
Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise(More)
A fundamental problem of modelling in Systems Biology is to precisely characterise quantitative parameters, which are hard to measure experimentally. For this reason, it is common practise to estimate these parameter values, using evolutionary and other techniques, by fitting the model behaviour to given data. In this contribution, we extensively(More)
The way how cell signals are generated, encoded, transferred, modified, and utilised is essential for understanding information processing inside living organisms. The tremendously growing biological knowledge about proteins and their interactions draws a more and more detailed image of a complex functional network. Considering signalling networks as(More)
When assuming a well stirred reactor and known macroscopic kinetic rates for mass action kinetics, microscopic rate constants for SRSim can be calculated. Prerequisite is knowing the characteristic geometric tolerances for the formation of bonds. In many cases, there will be no values available from biophysical or theoretical experiments yet. Even having(More)