Hamilton Institute Seminar

Wednesday, October 11, 2023 - 13:00 to 14:00
Hamilton Institute Seminar room (317), 3rd Floor Eolas Building, North Campus

Virtual participation: Zoom details available here

Speaker: Professor Pekka Orponen, Aalto University

Title: "Algorithmic Design of 3D Wireframe RNA Polyhedra"

Abstract: We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we have designed and characterised experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism.

Biography: Pekka Orponen is Professor of Computer Science at Aalto University, Finland. He received his PhD degree in Computer Science at the University of Helsinki in 1986. After a postdoctoral period at the University of Toronto, he held assistant and associate professorships at the University of Helsinki, before moving first to the University of Jyväskylä (1996-2001) and then to the Helsinki University of Technology, now Aalto University (2001-present). He served as the founding Head of the Aalto Department of Information and Computer Science for 2008-2014, and then as Vice-Head for Research of the newly-established Aalto Department of Computer Science for 2015-2016.
His research background is in the areas of algorithms and complexity, with specific contributions spanning computational complexity theory, foundations of neural network and analog computation, stochastic algorithms and distributed sensor networks. Since about 2010, his main research interest has been the computational theory and algorithmic design of nucleic acid nanostructures.