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Natural Computing


G. Rozenberg
University of Leiden
Course Type
Group 2
4-7 giugno 2012
Natural Computing is an interdisciplinary field of research that investigates human-designed computing inspired by nature as well as computation taking place in nature, i.e., it investigates models, computational techniques, and computational technologies inspired by nature as well as it investigates phenomena/processes taking place in nature in terms of information processing. One of the research areas from the second strand of research is the computational nature of biochemical reactions. It is hoped that this line of research may contribute to a computational understanding of the functioning of the living cell, which is based on interactions between (a huge number of) individual reactions. These reactions are regulated, and the main regulation mechanisms are facilitation/acceleration and inhibition/retardation. The interactions between individual reactions take place through their influence on each other, and this influence happens through these two mechanisms. In this course we present a formal framework for the investigation of processes carried by biochemical reactions in living cells. We motivate this framework by explicitly stating a number of assumptions that hold for a great number of biochemical reactions, and we point out that these assumptions are very different from the ones underlying traditional models of computation. We discuss some basic properties of processes carried by biochemical reactions, and demonstrate how to capture and analyse, in our formal framework, some biochemistry related notions. Besides providing a formal framework for reasoning about processes instigated by biochemical reactions, the models discussed in the course are novel and attractive from the models of computation point of view. This is extensively discussed throughout the course. The course is of a tutorial style and self-contained, in particular no knowledge of biochemistry is required. The course is suited for master and PhD students as well as for researchers and faculty members. It is of interest to computer scientists and mathematicians interested in formal models of computation as well as to bioinformaticians, biochemists, and biologists interested in foundational/formal understanding of biological processes.



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