In 1994, a pioneering experiment by Leonard Adleman showed that DNA could be used to solve mathematical problems by exploiting its capability to store and process information and using molecular biology tools to perform arithmetic or logic operations on the encoded data. Since then, the interest of researchers in the area of (bio-)molecular computing has been growing continuously, taking the discipline well beyond the original idea of using biological molecules as fundamental components of computing devices.
Within molecular computing much work has been done on the study of theoretical models of DNA computation and their properties, such as Tom Head’s splicing systems, together with experimental work. Convergences with nanosciences, nanoengineering, synthetic biology have also been explored and exploited.
One of the most significant achievements of molecular computing, for example, has been its contribution to the understanding of self-assembly, which is among the key concepts in nanosciences.
The next step has been the passage from the molecular level to the cellular level. The living cell is perhaps the most outstanding self-organized, hierarchical, adaptable, economic and robust information processing system that we know, and cellular processes such as gene regulatory networks, protein-protein interaction networks, biological transport networks and signalling pathways can be studied from the point of view of information processing. This knowledge will also enable us to harness the cell as a “nano-bot”, which can be programmed to carry on specific tasks such as targeted drug delivery, housekeeping of chemical factories and coordination of bio-film scaffolding and self-assembling.
The following contributions on the theme of molecular and cellular computing describe some of the projects carried out in Europe, and can be grouped into three groups:
- The first group of papers mainly concern membrane computing, a new unconventional computing model that abstracts from the structure and functionality of the living cell, illustrating both the theoretical basis of the models introduced as well as applications in various fields. M. Gheorghe gives an overview of the field, then G. Franco and V. Manca describe a research project that aims to synthesize a minimal cell, starting from a model based on membrane systems. The third paper (Agrigoroaiei, Aman and Ciobanu) discusses operational semantics, and the notions of causality and mobility in membrane systems. Possible connections with quantum computing are discussed by Leporati. The next paper describes the goals and activities of a Spanish network on Biomolecular and Biocellular Computing, which is not limited to membrane systems, but includes networks of bioinspired processors, synthetic biology, computational biology and bioinformatics. The last paper in this group (Csuhaj-Varjú and Vaszil) is of a theoretical nature, and relates membrane systems to automata, focusing in particular on the distributed organization of components of living systems.
- The papers in the following group focus on biological information processing, based on chemical reactions (Hinze, Bodenstein, Heiland, and Schuster), the engineering of biological systems with a given behaviour (Arroyo, Gómez and Marijuán), and molecular information processors (Gruenert, Dittrich and Zauner). Chemical reactions and the robustness of living systems with respect to the possible failure of their components are the inspiration for architectural ideas for robust distributed systems (Mauri and Petre), middleware (Pazat, Priol and Tedeschi), self-adapting systems (Cuesta, Pérez-Sotelo and Ossowski), and services (Di Napoli, Giordano and Németh).
- Finally, the two closing papers describe projects for the development of a computing device based on bacterial colonies (Amos and the BACTOCOM consortium) and for modelling and simulating biosensors, with possible applications to nanomedicine.
University of Milano-Bicocca