PACE has investigated a novel basis for evolvable IT using complex chemical systems that self-organize and self-reproduce: artificial chemical cells. While it would have been premature for PACE to have aimed to deliver the first novel chemical cell, novel IT technology for programming semi-autonomous chemical systems has been established and effective architectures for artificial cells established, so that now this objective should be achievable in the near future. PACE has integrated and extended a suite of physical and chemical simulation tools and multiple scales to promote the design of information-intensive autonomous chemical systems. The project has evaluated the adaptive and evolutionary potential of chemical artificial cells and how they can be programmed to perform useful tasks for a chemically-active, "immersed" rather than embedded, IT. The project has constructed novel chemical systems, that can serve as an effective basis for reducing the complexity of artificial cells. PACE has developed and tested a novel digital electronic-chemical microprocessor technology in connection with a new machine architecture based on a real-time microscale feedback loop - the "omega machine" - on the hard task of bootstrapping chemistry towards artificial cell autonomous operation. PACE has also developed algorithms and the technology to optimize rather general experimental protocols, going well beyond evolutionary optimization techniques. The project has also constructed a platform for controlling and monitoring the self-assembly of multiple artificial cells, that have been functionalized by specific surface structures. Finally, much of the significant progress in PACE is attributable to the integration achieved via a whole range of scientific meetings at the newly formed European Center for Living Technology - now an autonomous lasting legacy of the PACE project.
1. Artificial cells: conception and simulation
PACE has integrated the conception, modeling and simulation of artificial chemical cells and their subsystems as complex information systems. This includes the formulation of a roadmap and graphical classification language for artificial cells. Physical self-assembly of components to microscale structures provides a powerful mechanism of constructive information processing. A coherent simulation perspective at various scales is provided through a virtual lab site integrating experience with a variety of novel (and established) simulation tools, in the design of artificial cells. The conceptual significance of artificial cells for future ICT is surveyed in the separate chapter ICT implications.
2. Artificial cell evolution and functionality
The adaptive and evolutionary potential of chemical artificial cells has been explored using a range of theoretical techniques and simulation tools. Novel simulation platforms have been developed that integrate physical self-assembly, chemical reactions and evolution of genetic subsystems. The fundamental evolvabilty and stable integration of simple artificial cell architectures has been established. Efficient simulation platforms have been established for investigating artificial cell functionality with the specific emphasis on controlled self-assembly based on molecular surface recognition (cf programmed self-assembly).
3. Chemical subsystems for artificial cells
Novel chemical systems reduce the complexity of artificial cells by integrating multiple features of the familiar families of biopolymers - in particular the catalipid systems, the PNA genetic information system, and the redox-ready thioDNA replication system. These systems have been prepared to be compatible with, tested and in part optimized using the the omega machine technology.
4. Microfluidic support systems for artificial cells
Artificial cell functionality can be complemented, to ease development, using electronic microfluidic technology. Significant developments of digital electronic chemical control technology for the cell-scale chemistry have taken place in PACE.
These developments support both the search for and integration of artiifical cell chemical functionality. Electronic chemical microprocessor technology has been employed to construct a new machine architecture based on a real-time microscale feedback loop - the "omega machine". The capabilities of this novel chemically active IT has been explored with applications first to the hard task of bootstrapping chemistry towards artificial cell autonomous operation.
5. Evolutionary optimization towards artificial cells
Artificial cells will be capable of autonomous evolution, but to produce the first artificial cell, and to optimize IT functions of artificial cells, the general problem of optimization of the self-organization of chemical systems must be addressed. Whereas section 2 addressed the intrinsic evolution of artificial cells, in this section we concentrate on techniques for their external evolutionary optimization.
A key concept is the evolutionary optimization of experimental protocols, in the simplest case mixing protocols. In contrast with conventional combinatorial optimization, the number of experiments is strongly limited, and theoretical work has revealed how to use the statistical information about the success for individual protocols optimally in the search for better ones. This development has many applications beyond artificial cell IT.
6. Programmed self-assembly of artificial cells
Vesicles provide a container for one family of artificial cells, so that vesicle self-assembly to higher order structures provides a prototypical example of the use of artificial cells - building blocks that will in future reproduce - in the design of complex microscale systems. The distribution of different recognition molecules (analagous to CAMS) on the surfaces of the vesicles can direct the self-assembly of specific structures. In this first stage of investigation, the raw potential of static expression of recognition molecules is investigated - developmental processing will also be possible for artificial chemical cells in future work, and expand the potential for using a limited range of artificial cells to build complex self-repairing structures.
7. Scientific activity at ECLT
The ECLT itself will be described in a separate chapter of this final report. Here we summarize the scientific achievements of the various kinds of meetings and activity at the ECLT.