CAREER: Bridging the gap between theoretical and experimental self-assembly through computational modeling

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The goal of this project is to develop software which enables techniques from theoretical modeling of self-assembling systems based on DNA nanotechnology to be developed and evaluated using rigorous molecular dynamics simulations, and then incorporated into physical molecular designs and implementations. The software to be developed will consist of a fully integrated suite of open source software which will create a seamless pathway for the design of self-assembling systems based on components called tiles, via a high-level programming language interface to an abstract tile assembly simulator, all the way through the final output of the fully specified DNA strands which have been verified via highly accurate and DNA specific molecular simulations. The second main component of the proposed work is the integration of theoretical techniques and designs for algorithmic self-assembling systems into DNA-based motifs, and the performance of extensive simulation-based experiments to develop molecular designs for components which yield systems that are more robust to error and varying environmental conditions than current systems, allowing them to be more scalable and widely utilized.Developing robust and scalable molecular self-assembling systems has the promise to greatly impact many aspects of science and technology, potentially enabling atomically precise manufacturing of materials with carefully specified properties, implementation of molecular "robots", and targeted drug delivery mechanisms which are able to diagnose and treat diseases in vivo. To realize the great promise of this field, it is important to recognize that it is fundamentally interdisciplinary and incorporates fields such as physics, chemistry, mathematics, computer science, and biochemical engineering, among others, and to foster the development of researchers experienced in these areas and also skilled at this interdisciplinary work. This project focuses on interdisciplinary collaboration and student education, includes the development of an interdisciplinary course ("Introduction to DNA Nanotechnology''), the hosting of interdisciplinary workshops for high school students and also for experienced researchers, conducting interdepartmental seminars, and the development of software which can be easily used by scientists from many disciplines to quickly become proficient in this area. This will help train extremely valuable researchers capable of synthesizing knowledge and techniques spanning many disciplines.This project will create a freely released software suite capable of automating the design of DNA-based self-assembling systems. The work will involve extending current simulation software to be massively parallelizable, allowing simulations to be run across large supercomputing clusters, and the creation of new software modules able to perform automated, quantitative analyses of simulation results. Additional modules will be created to enable the suite to provide an end-to-end solution from theoretical design to simulation-based validation, along with an easily used web-based front end and database storage of results. The theoretical aspects of the project will involve incorporation of various theoretical construction techniques into molecular designs, and validation of those designs. Some specific theoretical techniques which will be exploited and evaluated include the incorporation of geometric hindrance to enforce correct algorithmic behavior, and hierarchical self-assembly.