Abstract Booklet ONLINE EVENT 26th International Conference on DNA Computing and Molecular Programming 14–17 September 2020 IOP webinars for the physics community dna26.iopconfs.org/ Contents Committees 2 Sponsors 3 Proceedings 3 Programme 4 Poster programme 8 Keynote presentations 11 Contributed presentations 17 Poster sessions 48 1 Committees Chairs • Andrew Phillips, Microsoft Research, Cambridge, UK • Andrew Turberfield, Department of Physics, University of Oxford, UK Programme Chairs • Cody Geary, Interdisciplinary Nanoscience Centre, University of Aarhus, Denmark • Matthew Patitz, Department of Computer Science and Computer Engineering, University of Arkansas Steering Committee • Luca Cardelli, Computer Science, Oxford University, UK • Anne Condon (Chair), Computer Science, University of British Columbia, Canada • Masami Hagiya, Computer Science, University of Tokyo, Japan • Natasha Jonoska, Mathematics, University of Southern Florida, USA • Lila Kari, Computer Science, University of Waterloo, Canada • Chengde Mao, Chemistry, Purdue University, USA • Satoshi Murata, Robotics, Tohoku University, Japan • John H. Reif, Computer Science, Duke University, USA • Grzegorz Rozenberg, Computer Science, University of Leiden, The Netherlands • Rebecca Schulman, Chemical and Biomolecular Engineering, Johns Hopkins University, USA • Nadrian C. Seeman, Chemistry, New York University, USA • Friedrich Simmel, Physics, Technical University Munich, Germany • David Soloveichik, Electrical and Computer Engineering, The University of Texas at Austin, USA • Andrew J. Turberfield, Physics, Oxford University, UK • Erik Winfree, Computer Science, Computation and Neural Systems, Caltech, USA • Damien Woods, Computer Science and Hamilton Institute, Maynooth University, Ireland • Hao Yan, Chemistry and Biochemistry, Arizona State University, USA Programme Committee • Ebbe Andersen Department of Molecular Biology and Genetics, Aarhus University • Luca Cardelli Department of Computer Science, University of Oxford • Yuan-Jyue Chen Electrical Engineering, Microsoft Research, Redmond • Anne Condon Computer Science, University of British Columbia • David Doty Computer Science, University of California, Davis • Elisa Franco Mechanical Engineering, University of California, Los Angeles • Cody Geary (co-chair) Interdisciplinary Nanoscience Center, Aarhus University • Anthony Genot Physics, CNRS • Manoj Gopalkrishnan Electrical Engineering, Indian Institute of Technology, Bombay • Elton Graugnard Materials Science and Engineering, Boise State University • Masami Hagiya Computer Science, University of Tokyo • Rizal Hariadi Physics, Arizona State University • Natasha Jonoska Mathematics, University of South Florida • Lila Kari Computer Science, University of Waterloo • Matthew Lakin Computer Science, University of New Mexico • Chenxiang Lin Cell Biology, Yale • Yan Liu Molecular Sciences, Chemistry and Biochemistry, Arizona State University • Olgica Milenkovic Electrical and Computer Engineering, University of Illinois • Satoshi Murata Mechanical Engineering, Tohoku University • Pekka Orponen Computer Science, Aalto University • Tom Ouldridge Applied Mathematics, Imperial College London • Matthew Patitz (co-chair) Computer Science and Computer Engineering, University of Arkansas, Fayetteville • Lulu Qian Bioengineering, California Institute of Technology • John Reif Computer Science, Duke University • Dominic Scalise Computer Science, Johns Hopkins University • Nicolas Schabanel Computer Science, CNRS and École normale supérieure de Lyon • Joseph Schaeffer Computer Science, Autodesk Research • Robbie Schweller Computer Science, University of Texas Rio Grande Valley • William Shih Biological Chemistry and Molecular Pharmacology, Wyss Institute at Harvard • David Soloveichik Electrical and Computer Engineering, University of Texas, Austin • Darko Stefanovic Computer Science, University of New Mexico • Jamie Stewart Engineering and Applied Science, California Institute of Technology • Petr Sulc Center for Biological Physics, Arizona State University • Chris Thachuk Computing and Mathematical Sciences, California Institute of Technology • Greg Tikhomirov Bioengineering, California Institute of Technology • Andrew Turberfield Physics, Oxford University • Bryan Wei School of Life Sciences, Tsinghua University • Shelley Wickham Chemistry & Physics, University of Sydney • Erik Winfree Computer Science, Bioengineering, Computation & Neural Systems, California Institute of Technology • Damien Woods Computer Science, Maynooth University • Fei Zhang Chemistry, Rutgers University Sponsors Proceedings The proceedings volume of DNA 26 is now officially published as volume 174 of LIPIcs and available at: https://drops.dagstuhl.de/opus/portals/lipics/index.php?semnr=16163 26th International Conference on DNA Computing and Molecular Programming 14–17 September 2020 ONLINE IOP webinars for the physics community EVENT Programme BST / UTC + 01:00 Monday 14 September Session 1 09:00 Overview of online conference system 09:15 Keynote: Weakly Computing with Petri Nets Jérôme Leroux, Université de Bordeaux, France 10:15 Break 10:25 A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures (Track B) Stefan Badelt, Casey Grun, Karthik Sarma, Brian Wolfe, Seung Woo Shin and Erik Winfree 10:50 Robust control of biochemical reaction networks via stochastic morphing (Track B) Tomislav Plesa, Guy-Bart Stan, Thomas E Ouldridge and Wooli Bae 11:15 Break 11:30 CRNs exposed: A Method for the Systematic Exploration of Chemical Reaction Networks (Track A) Marko Vasic, David Soloveichik and Sarfraz Khurshid 11:55 Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts (Track A) Antti Lankinen, Ismael Mullor Ruiz and Thomas E Ouldridge 12:20 Networking/Social 12:45 Break Session 2 15:00 Introduction 15:10 Algorithmic Design of 3D Wireframe RNA Polyhedra (Track C) Antti Elonen, Ashwin K Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C Simmel, Anton Kuzyk and Pekka Orponen 15:25 The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes (Track A) Abdulmelik Mohammed, Nataša Jonoska and Masahico 15:50 Break 16:05 New tools for online design, optimization, and simulation of large DNA, RNA and DNA-protein hybrid nanostructures (Track B) Erik Poppleton, Michael Matthies, Joakim Bohlin, Roger Romero, Jonah Procyk and Petr Sulc 26th International Conference on DNA Computing and Molecular Programming 16:30 scadnano: A browser-based, scriptable tool for designing DNA nanostructures (Track A) David Doty, Benjamin L Lee and Tristan Stérin 16:55 Break 17:05 Keynote: Bottom-up Construction of Cellular Functions using DNA Nanotechnology Tom de Greef, Eindhoven Institute of Technology, the Netherlands 18:05 Networking/Social 18:30 Close Tuesday 15 September Session 3 09:00 Poster session A 10:15 Keynote: Probabilistic verification and synthesis for reliable molecular circuit designs Marta Kwiatkowska, University of Oxford, UK 11:15 Break 11:25 DNA-templated heptameric α-helical barrel (Track B) Juan Jin, Emily G Baker, Jonathan Bath, Erik Benson, Derek N Woolfson and Andrew J Turberfield 11:50 Turning Machines (Track A) Irina Kostitsyna, Cai Wood and Damien Woods 12:20 Networking/Social 12:45 Break Session 4 15:00 A biochemical DNA nanoscope that identifies and localizes over a hundred unique features with nanometer accuracy (Track B) Nikhil Gopalkrishnan, Sukanya Punthambaker, Thomas Schaus, George Church and Peng Yin 15:25 Supervised learning in a multi-layer, non-linear chemical neural network (Track C) David Arredondo and Matthew R Lakin 15:40 Break 15:50 Keynote: 21 molecular algorithms using reprogrammable DNA self-assembly Damien Woods, Maynooth University, Ireland 16:50 Poster session B 18:05 Networking/Social 18:30 Close 26th International Conference on DNA Computing and Molecular Programming Wednesday 16 September Session 5 09:00 Keynote: Simplicity bias in self assembly and deep learning Ard Louis, University of Oxford, UK 10:00 Break 10:10 Coarse-Grained Simulation of DNA Hydrogel Structures (Track C) Oliver Henrich, Yair Augusto, Gutierrez Fosado, Zhongyang Xing, Magdalena and Erika Eiser 10:25 Characterising DNA T-motifs by Simulation and Experiment (Track B) Behnam Najafi, Katherine G Young, Jonathan Bath, Ard Louis, Jonathan Doye, and Andrew Turberfield 10:50 Poster session C 12:05 Networking/Social 12:30 Break Session 6 15:00 ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly (Track A) Titus H Klinge, James I Lathrop, Sonia Moreno, Hugh D Potter, Narun K Raman and Matthew R Riley 15:25 Robust heterochiral strand displacement using leakless translators (Track B) Tracy L Mallette, Milan N Stojanovic, Darko Stefanovic and Matthew R Lakin 15:50 Break 16:05 Composable Computation in Leaderless, Discrete Chemical Reaction Networks (Track A) Hooman Hashemi, Ben Chugg and Anne Condon 16:30 Programming and Simulating Chemical Reaction Networks on a Surface (Track B) Samuel Clamons, Lulu Qian and Erik Winfree 16:55 Poster session D 18:10 Networking/Social 18:30 Close Thursday 17 September Session 7 09:00 DNA origami bricks: A programmable monomer for hierarchical assembly in 3D (Track B) Minh Tri Luu, Ali Abbas and Shelley F Wickham 09:25 Design automation of Polyomino Set that Self-Assembles into a Desired Shape (Track A) Yuta Matsumura, Ibuki Kawamata and Satoshi Murata 26th International Conference on DNA Computing and