VIEWS (2004-2009)

Computational Views on Membranes and Ciliates

The NWO funded project 635.100.006 ``VIEWS'' is a cooperation between the Universiteit Leiden institutes Leiden Institute of Advanced Computer Science (Robert Brijder, dr. Francesco Bernardini, prof.dr. J.N. Kok, prof.dr. G. Rozenberg, dr. H.J. Hoogeboom) Institute for Biology (prof.dr. H. Spaink) and Mathematical Institute (Michael Muskulus, prof.dr. S.M. Verduyn Lunel, dr. F. Merkl, dr. S. Hille).

Outcome

Several papers were written under the funding of this project. Most importantly, the project resulted in the PhD theses of the two PhD students supported by VIEWS.

R. Brijder (2008). Models of natural computation: gene assembly and membrane system. Date of defence 3-12-2008. ISBN 978-90-9023428-1.
M. Muskulus (2010). Distance-based analysis of dynamical systems and time series by optimal transport. Date of defence 11-2-2010. ISBN 978-90-5335-254-0.

Description of Proposed Research

The aim of the project is to study basic aspects of life processes. The novelty of the research is the principal point of view that a number of basic life processes can be considered as computations. This point of view turned out to be very succesful in research in biology. Especially, in the area of Natural Computing, which has two `faces': computing going on in nature, and human designed computing inspired by nature. This interdisciplinarity research involves three areas of science: biology, computer science and mathematics.

In order to focus the research we have chosen two research topics which are representative for the two faces of the Natural Computing research: (i) Gene Assembly in Ciliates and (ii) Membrane Computing. The research on the computational nature of gene assembly has turned out to be already succesful in shedding light on the basic nature of this process, which is one of the most fascinating examples of basic life processes. The research on the second topic has led to very interesting models of computation inspired by the role of membranes in living cells.

Typically for research on "life processes as computation" point of view, the major mathematical tools used here come from discrete mathematics (rewriting systems, combinatorics of words, graph theory). One of the goals of our project is to investigate how this research can be enriched by applying more mathematical methods and techniques from probability and nonlinear analysis. For example, current research might be enriched by applying state-of-the-art methods from dynamical systems. We believe that new developments in the analysis of dynamical systems that possess a discrete spatial structure, i.e., cellular automata, coupled map lattices and lattice differential equations, can also be applied in the present setting.

An essential part of the project aims at getting a deeper and more complete biological insight into the above two research topics. In particular that means to understand the biomolecular implementation of various computational aspects of gene assembly (in other words, learning about the biological hardware - bioware - used by the ciliates to implement computation going on during gene assembly). Moreover for membrane computing we plan to redirect some research in into the realm of original biological motivation: the role and the functioning of biological membranes.

As a matter of fact through this project we want to strengthen (and to get a sound understanding of) the mutual feedback between biological, dynamical and computational research of basic life processes. In particular, the study of the qualitative behaviour of these processes leads to fundamental questions in the theory of dynamical systems and probability theory, which can only be solved in close interaction with computational science.

details:
projects within VIEWS
• Gene Assembly in Ciliates
• Membrane systems and their dynamics

publications

NWO proposal [.pdf]

poster [.pdf]
(NWO Computational Life Sciences Meeting, Utrecht, February 25, 2005)

march 2007