Petr Šulc: Molecular simulations to guide experimentally-realizable bionanotechnology devices

8th January 2024, 1 PM, J. Heyrovský Institute, Brdička Hall

The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of competing alternative structures or amorphous aggregates. The goal of inverse design problem in nanotechnology is hence to find a set of blocks that reliably self-assemble in high yield into a target structure while avoiding kinetic traps and alternative competing states. We present here a new design pipeline that usesmultiscale molecular simulations of DNA, RNA and proteins to design nanostructures and devices that can be successfully realized in lab. We show applications of our modeling pipeline to design of pyrochlore lattice, a highly coveted 3D lattice structure with promising applications in metamaterial applications.

We further show examples of designing finite-size polycube nanostructures built from cube-shaped subunits, and design of self-assembling capsids. We show preliminaryexperimental results showing successful assembly of these designs using DNA nanotechnology. We further discuss examples of other recent applications of our design tools: a chemically powered oscillatingnanoengine, multivalent nanosynbodies that inhibit SARS-CoV-2 spike protein binding, and cytodirect platform for targeted delivery oftherapeutic payloads.

Petr Šulc is an Assistant Professor at Arizona State University. He received his bachelor's degree in mathematical engineering at Czech Technical University in 2006, his master's degree in quantum physics at Ecole Polytechnique, Paris, in 2009, and his D.Phil. degree in theoretical physics at University of Oxford in 2014. In 2018, he established his research group at the Biodesign Institute at Arizona State University. His research broadly encompasses applications of statistical physics and computational modeling to studies of DNA and RNA in biology and nanotechnology. He is a recipient of NSF CAREER award and ERC starting grant.