Virtual participation: Zoom details available here
Speaker: Dr Shinnosuke Seki, University of Electro-Communications, Tokyo
Title: "RNA co-transcriptionality: How can/should we program RNA for computations?"
Abstract: Being responsible for computing to sustain life and inheritable via genes, RNAs are a reasonable choice as a material for artificial in vivo computers. They compute in nature by folding “co-transcriptionally,” and co-transcriptional folding (CF) has proven promising as a platform for programming at least in vitro. An RNA strand is constituted of nucleotides with bases A, C, G, U whose composition endows the strand with a chemical direction noted as 5’ -> 3’. RNA strands hybridize, that is, coil around each other in an antiparallel manner and stabilize by being zipped base by base as A-U and C-G into a cylindrical structure called a helix. An RNA strand folds while being synthesized from its DNA template sequentially (transcription). Geary, Rothemund, and Andersen have demonstrated in vitro that CF enables an RNA strand to fold hierarchically by having pre-designated factors, or domains, hybridize, and then the resulting helices be organized further via various structural and computational motifs, and successfully programmed a 2-dimensional rectangular tile-like structure (RNA origami architecture) into a template via a hierarchical CF pathway. This “Hello World!” program raises the problem of how to program rather a computation in CF. Using a simple computation programmed in a computational model of CF as a case study, this talk will articulate the issues to be discussed and overcome for further advancement of this programming platform.
Biography: Having received his PhD. in computer science from the University of Western Ontario (London, ON, Canada) in 2010, he had worked as a postdoctoral researcher in Kyoto University (Japan), Aalto University (Espoo, Finland), and for the Academy of Finland (AF, renamed Research Council of Finland, or RCF) until having been appointed as a faculty at the University of Electro-Communications, Tokyo in 2015. As the PI of the AF project on “Practical design of molecular self-assembly systems and their optimization,” he modeled RNA co-transcriptional folding mathematically, and demonstrated its potential as a driving principle for general-purpose in vivo computations. He has organized two international conferences so far (DLT2018 and UCNC2019), served for DNA30 in 2024 as a PC co-chair, and been steering UCNC (Int’l Conf. on Unconventional Computation and Natural Computation) since 2021. His research interests include, but not limited to, molecular programming, RNA co-transcriptionality, and theory of automata and formal languages.