Thomas Hinze

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BACKGROUND 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(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)
The rapid developments in the eld of DNA computing reeects two substantial questions: 1. Which models for DNA based computation are really universal? 2. Which model fulllls the requirements to a universal lab-practicable programmable DNA computer that is based on one of these models? This paper introduces the functional model DNA-Haskell focussing its(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)
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)
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)