2010.03.08 | Arne Nis Jensen

Distinguished Lecture: Grzegorz Rozenberg, Leiden University

Computational Nature of Processes Based on Biochemical Reactions

Abstract:

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 the two mechanisms mentioned above.

In our lecture we present a formal framework for the investigation of biochemical reactions - it is based on reaction systems. We motivate this framework by explicitely stating a number of assumptions/axioms 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 in reaction systems, and demonstrate how to capture and analyse, in our formal framework, some biochemistry related notions.

The lecture is of a tutorial style and self-contained, in particular no knowledge of biochemistry is required.

About the speaker:

Professor G. Rozenberg is one of the most influential persons within theoretical computer science. He has published 500 papers, 6 books, and is a (co-)editor of more than 70 books. He was the President of the European Association for Theoretical Computer Science (EATCS) in 1985-1994. He is editor-in-chief for five journals and book series including Theoretical Computer Science. He is the head of the Theoretical Computer Science group at Leiden Institute of Advanced Computer Science (LIACS), and the scientific director of Leiden Center for Natural Computing (LCNC).

His current research interests are:

- natural computing, including molecular computing, computation in living cells, self-assembly, and theory of biochemical reactions.

- theory of concurrent systems, in particular theory of Petri nets, theory of transition systems, and theory of traces.

- theory of graph transformations.

- formal language and automata theory.

- mathematical structures useful in computer science, in particular theory of 2-structures.

- computer supported cooperative work.