Development in humans and other higher organisms creates complex, precisely defined multicellular structures and patterns. These structures are the result of molecular programs that are stored in the sequences and concentrations of biomolecules and are executed when molecules interact and change state through chemical reactions. The goal of this proposal is to understand how biochemical systems can be reliably programmed to form asymmetric patterns with multiple layers of organization. This proposal is part of a general goal to understand how to program global behavior and structure based on local rules, which a key intellectual challenge in many areas of computer science.
The PI's propose that complex, hierarchical chemical patterns can be formed by systems in which the molecules collectively execute a molecular program for pattern formation. The PI's will develop a chemical programming language in which information from simple input patterns is integrated by logical operations to form new pattern regions. These logical operations are then systematically integrated into larger programs, allowing the generation of patterns with complex, multiscale structure similar to that seen in biology. Designed synthetic DNA molecules that together act as circuit elements will be used to implement this language. DNA molecules are ideal substrates for a molecular programming approach because they have complex sequences with predictable behaviors and interactions. This research is tightly integrated with an outreach program that will develop an educational program dedicated to teaching the interdisciplinary skills that are necessary to be successful in molecular programming. ,
