Collaborative Research: FET: Medium: Algorithmic Shape Encoding at the Nanoscale

Algorithms permeate our modern world, driving everything from navigation, information storage, and data retrieval. In contrast, biological information is inherently physical, carried by molecules whose shapes determine their interactions with the environment. This NSF-funded program aims to explore and harness the interface between the deoxyribonucleic acid (DNA) “software” and the geometric “wetware” of molecules. The research will begin by developing mathematical tools to distinguish molecules based on their 3D shapes and structures. These tools will then be used to create a new programming framework: “algorithmic shape encoding.” Using small DNA tiles as modular pieces in a molecular-scale 3D jigsaw puzzle, the team will construct increasingly complex structures—drawing inspiration from nature’s ability to link form and function. The expected outcomes include breakthroughs in self-assembling materials, biocomputing, and optical communication systems. In addition to scientific discovery, this program will foster interdisciplinary training across mathematics, engineering, and chemistry from high school to the postdoctoral levels. DNA, with its predictable structure and ability to self-organize at nanometer precision, offers a powerful platform for designing next-generation materials. This project builds on the well-established tensegrity triangle motif to create a diverse set of 3D DNA motifs that self-organize into authentic 3D DNA building blocks. In Aim 1—Unit Design: Encoding Information in 3D DNA Motifs—researchers will identify key structural features of DNA motifs that can encode information through molecular shape. This will involve developing computational tools to predict and constrain topologies and verifying motif structures using X-ray and related techniques. In Aim 2—Algorithmic Shape Encoding for Large 3D Nanomaterials—the focus will shift from individual motifs to overall structural organization. The team will (1) design and characterize quaternary structures with defined chirality, and (2) develop periodic, hierarchical, and fractal-based arrays that require supramolecular-level algorithms rather than sequence-level design. Finally, the project will prototype optical materials capable of light-based computation and readout, paving the way for new advances in nanomaterials and biomimetic systems. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.