Autonomous Computing Artificial Cells

ongoing

We propose an ambitious 5-year multidisciplinary program that seeks to pioneer and establish a fundamentally new paradigm in molecular information systems that is based on novel conceptual and experimental advances on the integration of DNA-based chemical reaction networks (CRNs) and semipermeable microcapsules, i.e. protocells. In AutonoMous computInG Artificial cells (AMIGA), we will establish a platform technology, based on molecular communication between interacting protocells, capable of revolutionary new modes of molecular sensing, computation and data storage/retrieval. Progress in this emerging field requires i) the development of computer-aided design (CAD) strategies to implement large-scale CRNs consisting of hundreds of components, ii) formulating suitable micro-substrates, such as droplets or vesicles, to spatially localize CRNs and ways to manipulate their interconnection and iii) strategies that allow direct recording of molecular operations onto a chemical storage medium such as DNA. We address these challenges via a comprehensive research program in which we implement large-scale, DNA-based CRNs by localization of components in interacting protocells resulting in distributed molecular circuits programmed to display advanced computational functions such as (i) asynchronous logic, (ii) integral feedback control and (iii) molecular pattern recognition. Combining protocell localization with recent advances in CRISPR base editors, we will construct an integrated system where molecular operations can write instructions on permanent memory storage elements. The developed methodology finds applications in emerging technologies aimed at using molecular circuits for in-vitro diagnostics and the use of synthetic DNA as a storage medium for digital data.