A formal framework for processes inspired by the functioning of living cells: Natural Computing approach

Lecturer: Professor Grzegorz Rozenberg (Leiden University, The Netherlands and University of Colorado at Boulder, USA).

About the lecturer | Course Summary | Course Structure | Overview Lecture | Assignment

About the lecturer: G.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:

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 and natural computing in Europe. He is a Foreign Member of the Finnish Academy of Sciences and Letters, a member of Academia Europaea, and he received Honorary Doctorates from 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.

Course summary: Natural Computing is an interdisciplinary research field 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 research areas from the second strand of research is a computational understanding of the functioning of the living cell. We view this functioning in terms of formal processes resulting from interactions between (a huge number of) individual reactions. These interactions are driven by two mechanisms, facilitation and inhibition: reactions may (through their products) facilitate or inhibit each other. 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 these processes, and we point out that these assumptions are very different from the ones underlying traditional models of computation. We discuss some basic properties of these processes, and demonstrate how to capture and analyse, in our formal framework, some notions related to cell biology and biochemistry. Research topics in this framework are motivated by biological motivations and the need to understand the underlying computations. The models we discuss turned out to be novel and attractive from the theory of computation point of view.

The course is of a tutorial style and self-contained, in particular no prior knowledge of biochemistry or cell biology is required. It 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.

Course structure: The course will be given in three one-day blocks, covering:


Overview lecture: On Nov. 27, Prof. Rozenberg will give an overview lecture that will present the general area related to the course. The lecture will be organized at IPI PAN:

Tuesday, Nov. 27, 14:30
IPI PAN, large lecture hall (ground floor)
ul. Jana Kazimierza 5
01-248 Warszawa

The course covers and extends in a systematic way and in great detail the material presented in the overview lecture. Although the overview lecture is obviously useful for the participants of the course, one does not have to attend it in order to attend the course - the course itself is self-contained.

Please send the solution (pdf) to Bartek Klin (klin AT[you-know-what]) by 4 January, 2013.