Grzegorz Rozenberg: Natural Computing Lectures

A FORMAL FRAMEWORK FOR PROCESSES INSPIRED BY THE FUNCTIONING OF LIVING CELLS: NATURAL COMPUTING APPROACH

Prof. Dr. Grzegorz Rozenberg
Leiden Institute of Advanced Computer Science (LIACS)
Leiden Center for Natural Computing (LCNC)
Leiden University, The Netherlands
and
Department of Computer Science
University of Colorado at Boulder, USA


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 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.

A short CV of Grzegorz Rozenberg

Grzegorz Rozenberg is a Professor of Computer Science at Leiden University, The Netherlands, and an Adjunct Professor at the Department of Computer Science of University of Colorado at Boulder, U.S.A. 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).
He has published more than 500 papers, 6 books, and is a (co-)editor of about 90 books.

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

He is an editor-in-chief of a number of journals and book series. He is a member of an editorial board of about 20 journals and book series. He edited four handbooks in the areas of theoretical computer science and natural computing.

He was the President or the Steering Committee Chairman of a number of renowned organizations and conferences in the areas of computer science, natural computing, and nanoscience (among others, the President of the European Association for Theoretical Computer Science; the President of the International Society for Nanoscale Science, Computation and Engineering; the Chairman of the Steering Committee for DNA Computing Conference; and the Chairman of the Steering Committee for the International Conference on Theory and Applications of Petri Nets). He has been a member of the program committees and invited speaker for practically all major conferences in theoretical computer science in Europe.

He is a Foreign Member of the Finnish Academy of Sciences and Letters, a member of Academia Europaea, and he is holder of Honorary Doctorates of the University of Turku, Finland, the Technical University of Berlin, Germany, and the University of Bologna, Italy. He has received the Distinguished Achievements Award of the European Association for Theoretical Computer Science "in recognition of his outstanding scientific contributions to theoretical computer science". He is a Highly Cited Researcher by ISI.