Computational Design Principles for Functional DNA-based Materials

Project Personnel

Mark Bathe

Principal Investigator

Massachusetts Institute of Technology (MIT)


Peng Yin

Harvard University


Hao Yan

Arizona State University


Funding Divisions

Civil, Mechanical and Manufacturing Innovation (CMMI)

This grant provides funding for the development of a computational tool to determine optimal design parameters for the synthesis of DNA-based materials. The developed tool will determine the optimal DNA sequences and environmental assembly conditions, including solvent and temperature, to realize pre-specified design criteria for two-dimensional and three-dimensional DNA-based nanoscale structures and materials. Physics-based computational models will be used to incorporate mechanical, electrostatic, and hybridization free energies into an overall structural-thermodynamic model of the target DNA-based assembly. This model will be used together with numerical optimization and highly parallel computation to optimize the design and synthesis process. Detailed experimentation will be used to test and validate the computational tool, including two-dimensional and three-dimensional characterization of target structural properties and assembly kinetics. The results of this research will lead to a broadly accessible, automated design tool for the production of custom DNA-based nanostructures and materials.