EAGER: Algorithmic aspects of molecular circuits and molecular machines

Stanford University, Stanford CA

Investigators

Abstract

Project Summary Proposal #: 0947670 PI: Ashish Goel We are used to thinking of DNA as a biological molecule. However, DNA, its cousin the RNA, and other associated molecules such as enzymes, are also engineering building blocks. Think of them as ?combinatorial Legos? which fit together and inter-operate not just by mechanics and geometry but also using the chemical sequence imprinted on them. This has many revolutionary potential applications. This also poses many mathematical and algorithmic questions which are both interesting in their own right and also provide a framework to devise useful experimental techniques. The PI proposes to conduct research in the emerging field of ?molecular algorithms?, i.e., algorithms which are meant to be implemented on molecules. This study will proceed in two broad directions: molecular machines and molecular circuits. The two areas are linked both thematically and in terms of techniques. We will constantly consult with practitioners in this field, so that the results of this research are both novel and useful. Intellectual merit: Molecular algorithms require tools and techniques that are considerably different from traditional algorithms. We can not assume building blocks such as memories, actuators, sensors, transistors, processors etc; rather, these are often the things we are trying to devise using more basic primitives such as DNA hybridization, enzymatic reactions, and migration. Consequently, advances in molecular algorithms are likely to require novel mathematical techniques that will enrich the disciplines of coding theory, combinatorial algorithms, and probabilistic analysis. Broad impact: Molecular machines have been proposed as sensors, actuators, and drug delivery mechanisms. Molecular circuits have the potential to finely control other molecular processes. Much of the hard work in developing these ideas is being done by experimentalists. However, theoretical tools such as the one we propose to develop also have an important role to play in realizing the full potential of this area and in deciding upon the most promising experimental directions. In addition, molecular algorithms could facilitate sophisticated tasks such as counting, shape recognition, precisely controlled crystal growth etc. at nano-scales. The PI has developed a class in molecular algorithms which he will update and teach bi-annually. Also, many graduate students will receive valuable research experience in this important area.