Elements of Computational Systems Biology

5

A (NATURAL) COMPUTING PERSPECTIVE ON CELLULAR PROCESSES

Matteo Cavaliere and Tommaso Mazza

The Microsoft Research - University of Trento, CoSBi, Trento, Italy

5.1 NATURAL COMPUTING AND COMPUTATIONAL BIOLOGY

Natural computing is a fast growing field of interdisciplinary research driven by the idea that natural processes can be used for implementing computations, constructing new computing devices, and to get inspirations for new computational paradigms. Moreover, natural computing can also be understood as abstracting biological processes in form of computational processes to allow the use of computational tools for analyzing biologically relevant properties. The field is growing very fast (see, the journals in the area, e.g., [1] and [2]). This chapter is constructed on the same double vision: In the first part of the chapter, we recall a computational model inspired by the structure and the functioning of living cells, called membrane system, and we show how one can abstract biologically relevant properties and study them by using tools coming from theoretical computer science. In the second part of the chapter, we show how the paradigm can be extended and adapted in order to describe and simulate the mechanisms underlying cell cycle and breast tumor growth.

5.2 MEMBRANE COMPUTING

An important research direction in natural computing concerns computations in living cells. An abstract computational model inspired by the structure and the functioning of living cells is a membrane ...