DNA 25


Schedule Keynote Speakers Posters

The conference will move between a few different locations. Although we will try to remind you, please make sure to check the schedule and location. Events are held in the location listed for the entire day, unless otherwise noted.

Note that the HUB, Allen Center and Gates Center are all within a 2 min walk from each other on Stephens Way at the center of the UW campus. Alder Commons is about a 10-15 min walk from these.

Participants are expected to follow the Code of Conduct.


Monday, August 5

Husky Union Building (HUB) - Room 160 (Lyceum)
1:30p Introduction and Welcome
Afternoon Session
Chair: Georg Seelig
1:40p Keynote 1 -- David Baker: The Coming of Age of De Novo Protein Design
Modular design of functional RNA origami scaffolds
Cody Geary, Guido Grossi, Paul Rothemund and Ebbe Sloth Andersen
Combinatoric Catalytic Reaction Networks
William Poole
3:20p BREAK
Chemical reaction networks and stochastic local search
Erik Winfree
A reaction network scheme which implements inference and learning for Hidden Markov Models
Abhinav Singh, Carsten Wiuf, Abhishek Behra and Manoj Gopalkrishnan
Implementing arbitrary CRNs using strand displacing polymerase
Shalin Shah, Tianqi Song, Xin Song, Ming Yang and John Reif
4:55p End of session
5:00p Poster session 1 and Opening Reception - Atrium of Paul G. Allen Center

Tuesday, August 6

Husky Union Building (HUB) - Room 160 (Lyceum)
8:30a Light continental breakfast
Morning Session
Chair: Ned Seeman
9:00a Keynote 2 -- Michael Elowitz: Protein Circuit Designs for Computation and Communication
Molecular program for isothermal digital detection of microRNA
Guillaume Gines, Roberta Menezes, Thomas Jet, Valérie Taly and Yannick Rondelez
Designing switchable Cas12a guide RNAs
Lukas Oesinghaus and Friedrich Simmel
10:40a BREAK
A smart polymer for sequence-selective binding, pulldown and release of DNA targets
Elisha Krieg, Krishna Gupta, Andreas Dahl, Mathias Lesche, Susanne Boye, Albena Lederer and William Shih
Sequence selective activation of conditional small interfering RNAs by RNA transcripts in mammalian cells
Si-Ping Han, Lisa Scherer, Ane Salvador-Garicano, Matt Gethers, Marwa Ben Haj Salah, Rebecca Mancusi, Sahil Sagar, Robin Hu, Julia Derogatis, Ya-Huei Kuo, Guido Marcucci, Saumya Das, John Rossi and William A. Goddard Iii
Thioflavin-T as a Fluorogenic Small-Molecule Probe for DNA Circuits
Peter Allen, Tulsi Damase, Md. Mamunul Islam and Mason Shipley
12:25p LUNCH - Lyceum
Afternoon Session
Chair: Lulu Qian
2:00p Keynote 3 -- Dana Randall: Phase Transitions in Distributed and Stochastic Algorithms
Toward Catalytic Networks from Thermodynamic Binding Networks
Keenan Breik, Cameron Chalk, David Doty, David Haley and David Soloveichik
3:15p BREAK
DNA Nanostructures Coordinate Gene Silencing in Mature Plants
Huan Zhang, Gözde Demirer, Honglu Zhang, Tianzheng Ye, Natalie Goh, Abhishek Jindal Aditham, Frankie Cunningham, Chunhai Fan and Markita Landry
DNA Nanostructures that Self-Heal in Serum
Yi Li and Rebecca Schulman
Automated Design of Curved DNA Origami Nano-Capsules with Specific Shape and Variable Multilayer-Reinforced Rigidity
Daniel Fu, Raghu Narayanan Pradeep, Fei Zhang, John Schreck, Hao Yan and John Reif
4:55p End of session
5:00p Poster session 2 - Atrium of Paul G. Allen Center

Wednesday, August 7

Alder Hall - Alder Commons (1st floor)
8:30a Light continental breakfast
Morning Session
Chair: Luca Cardelli
9:00a Keynote 4 -- Anne Shiu: Design Principles of Biochemical Reaction Systems
Kinetic control of spontaneous nucleation in uniquely-addressed multifarious self-assembly
Constantine Evans, Jackson O'Brien, Erik Winfree and Arvind Murugan
Crisscross Cooperative Assembly
Chris Wintersinger and Dionis Minev
10:40a BREAK
DNA Reaction-Diffusion Attractor Patterns
Phillip Dorsey and Rebecca Schulman
Non-cooperatively assembling large structures
Damien Regnault and Pierre-Étienne Meunier
Simulation of Programmable Matter Systems Using Active Tile-Based Self-Assembly
John Alumbaugh, Joshua Daymude, Erik Demaine, Matthew Patitz and Andrea Richa
12:25p LUNCH
Afternoon Session
Chair: David Soloveichik
Real-Time Equivalence of Chemical Reaction Networks and Analog Computers
Xiang Huang, Titus Klinge and James Lathrop
Reversible computation using swap reactions on a surface
Sean Yu, Gokul Gowri, Tatiana Brailovskaya and Erik Winfree
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains
Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Cote, Mark Schmidt and Anne Condon
3:15p BREAK
Error-free stable computation with polymer-supplemented chemical reaction networks
Allison Tai and Anne Condon
Combined amplification and molecular classification for gene expression diagnostics
Gokul Gowri, Randolph Lopez and Georg Seelig
Autonomous in situ generation of multi-stranded RNA complexes for synthetic molecular circuits
Wooli Bae, Thomas Ouldridge and Guy-Bart Stan
4:55p End of session

Thursday, August 8

Husky Union Building (HUB) - Room 160 (Lyceum)
8:30a Light continental breakfast
Morning Session
Chair: Erik Winfree
9:00a Keynote 5 -- Leonard Adleman: Genes, Memes, Cenes
New bounds on the tile complexity of thin rectangles at temperature-1
Scott Summers, David Furcy and Christian Wendlandt
Design automation for DNA origami mechanisms
Chao-Min Huang, Anjelica Kucinic, Carlos Castro and Hai-Jun Su
10:40a BREAK
Solid-State Nanopore-Based DNA Data Storage and DNA Computing
Kaikai Chen, Jinglin Kong, Jinbo Zhu, Niklas Ermann, Paul Predki and Ulrich F. Keyser
DNA Punch Cards: Encoding Data on Native DNA Sequences via Topological Modifications
Kasra Tabatabaei, Boya Wang, Nagendra Athreya, Behnam Enghiad, Alvaro Hernandez, Jean-Pierre Leburton, David Soloveichik, Huimin Zhao and Olgica Milenkovic
Developing Privileged Genetic Alphabets for DNA Information Storage
Raghav Shroff, Jared Ellefson, Alex Boulgakov, Randy Hughes, Edward Marcotte and Andrew Ellington
Probing the Physical Limits of Reliable DNA Data Retrieval
Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Karin Strauss and Luis Ceze
12:30 LUNCH - Lyceum
Afternoon Session
Chair: Karin Strauss
2:00p Keynote 6 -- Erik Winfree: 25 Years of Computing with DNA
SIMDNA: Single Instruction, Multiple Data Computation with DNA Strand Displacement Cascades
Boya Wang, Cameron Chalk and David Soloveichik
3:25p BREAK
Moderator: Andy Ellington
Panelists: Anne Condon, Ned Seeman, William Shih, Shelley Wickham
5:00p RECEPTION - Bill & Melinda Gates Center

Friday, August 9

Molecular Technology Day
Husky Union Building (HUB) - Room 160 (Lyceum)
8:30a Light continental breakfast
Morning Session
Chair: William Shih
Biocomputing in synthetic cells
Kate Adamal
Scalable molecular reporting with nanopore sensor arrays
Jeff Nivala
Construction of DNA Amplification Circuit for Directing DNA Nanodevices and Quantifying Nucleic Acids
Ken Komiya, Teruya Enomoto and Masayuki Yamamura
10:25a BREAK
Applications of programmable autonomous synthesis cascades with primer exchange reactions
Jocelyn Kishi
Enzymatic and chemical manipulation of nucleic acids: the 'Intel Inside' of DNA computing
Andy Ellington
12:05p End

Keynote Speakers

Genes, Memes, and Cenes

University of Southern California
Leonard Adleman

I was a young mathematics professor at MIT when I began reading Richard Dawkins’ 1976 book “The Selfish Gene” about the primacy of genes in Darwinian evolution. In the last chapter, Dawkins introduced what he called “memes” – analogues of genes that resided in peoples’ brains rather than in molecules of DNA. I recall saying to myself: Oh, that’s how it all works.

How what works? Pretty much everything. For example, you.

As a mathematician, I had long been aware of the work of logicians Alan Turing (the father of computer science) and Steven Kleene (the discoverer of the so called “recursion theorem”), and it had been apparent to me, and to others who cared about such things, that their results implied that the things stored in computers (which I later called cenes) were also analogues of genes.

I was really struck by all of this and ever since I have worked to put the pieces together.

It was clear from the start that genes, memes, and cenes must obey Darwin’s laws: survival of the fittest, mutation and natural selection. But with time it became clear that Darwin’s laws are often misunderstood, and that there are other laws, not previously described, that also apply. It also became clear that these laws did not just apply to genes, memes, and cenes, but to a larger class of things I came to call “prenes”

Genes have become central to the study of biological evolution. I believe that memes, cenes and other prenes have the potential to occupy a similar position with respect to the study of societal and computer evolution.

Note: The latest draft of Professor Adleman’s book Genes, Memes and Cenes can be downloaded from his webpage.

The Coming of Age of De Novo Protein Design

University of Washington
David Baker

Proteins mediate the critical processes of life and beautifully solve the challenges faced during the evolution of modern organisms. Our goal is to design a new generation of proteins that address current day problems not faced during evolution. In contrast to traditional protein engineering efforts, which have focused on modifying naturally occurring proteins, we design new proteins from scratch based on Anfinsen’s principle.

Protein Circuit Designs for Computation and Communication

California Institute of Technology
Michael Elowitz

Circuits of interacting proteins can perform a variety of “computational” functions in living cells. They allow cells to encode and decode signals, store information, and compute responses to complex stimuli. What kinds of design principles allow natural protein circuits to perform these functions effectively? How can we design synthetic protein circuits that provide similar or totally new functionality? This talk will explore emerging paradigms of natural and synthetic protein circuit design in mammalian cells. A major focus will be on core intercellular communication pathways such as BMP and Notch which use multiple promiscuously interacting ligands and receptors, as well as new approaches for programming fully synthetic mammalian circuits.

Phase Transitions in Distributed and Stochastic Algorithms

Georgia Institute of Technology
Dana Randall

Markov chain Monte Carlo methods have become ubiquitous across science and engineering to model dynamics and explore large combinatorial sets. One of the most striking discoveries has been the realization that many natural Markov chains undergo phase transitions whereby they abruptly change from being efficient to inefficient as some parameter of the system is modified, also revealing interesting properties of the underlying stationary distributions. We will explore valuable insights that phase transitions provide in three settings. First, they allow us to understand the limitations of certain classes of sampling algorithms, potentially leading to faster alternative approaches. Second, they reveal statistical properties of stationary distributions, giving insight into various models interacting agents. Third, they predict emergent phenomena that can be harnessed to design distributed algorithms for certain asynchronous models of programmable active matter and swarm robotics. We will see how these three research threads are closely interrelated and inform one another.

Design Principles of Biochemical Reaction Systems

Texas A&M University
Anne Shiu

How do signaling networks within cells process and encode information?

This talk investigate the theory side of this question, through the dynamical systems arising from biochemical networks. We focus specifically on two dynamical properties – bistability and oscillations – which may indicate that the underlying biochemical mechanism acts as a biological switch or clock. Our main mathematical tool is to harness a rational parametrization (that is, a map with rational-function coordinates) of the set of steady states of a system. We describe how such a parametrization allows us to analyze the dynamics of a large class of signaling networks involving phosphorylation and other forms of post-translational modification. Taken together, our results elucidate how bistability and oscillations emerge in important biological networks, and point to design principles for achieving such dynamics.

25 Years of Computing with DNA

California Institute of Technology
Erik Winfree

I was a graduate student floundering around for a thesis topic when Len Adleman published his remarkable paper on “Molecular computation of solutions to combinatorial problems” in 1994. That paper brought me together with Paul Rothemund, who had just received his undergraduate degree, and he introduced me to Ned Seeman’s incredible (even at the time!) body of work on DNA nanotechnology. One thing led to another, and Paul and I presented our ideas at the first workshop on DNA Based Computers at Princeton in April of 1995, where we met Len and Ned. Heady times, as they say. In this talk I will revisit some of the deeper ideas that were explored in those days, and trace their development from DNA computing through DNA nanotechnology and molecular programming and in some sense “back” to DNA data storage. I will emphasize “thinking like a physicist” and “thinking like a computer scientist”, as well as the interplay of theory and experiment. I will conclude with some probably way-off-the-mark conjectures about the future.


Both sessions will be held in the atrium of Paul G. Allen Center. Pizza and drinks will be served.

Maximum poster size is 3 feet tall, 4 feet wide (94 x 122 cm).

Monday Session

Toward Catalytic Networks from Thermodynamic Binding Networks
Keenan Breik, Cameron Chalk, David Doty, David Haley and David Soloveichik
DNA-Encircled Lipid Bilayers
Thorsten L Schmidt
A Programmable DNA Nano-indicator-based Platform for Large-scale Square Root Logic Biocomputing
Chunyang Zhou
Dynamic DNA materials powered by artificial metabolism
Shogo Hamada and Dan Luo
DNA nanostructure-based label-free detection of cancer miRNA-21 biomarker
Shuo Han, Shuo Yang, Wenyan Liu and Risheng Wang
Engineering Kinetically Uniform Sets of DNA Sequences
Michael Tobiason, Bernard Yurke and William Hughes
Developing Privileged Genetic Alphabets for DNA Information Storage
Raghav Shroff, Jared Ellefson, Alex Boulgakov, Randy Hughes, Edward Marcotte and Andrew Ellington
DNA-based logic gate array with alphanumeric readout
Ryan Connelly and Yulia Gerasimova
Engineering RNA-Sensing CRISPR-Cas Systems
Mike Jin, Nicolas Garreau de Loubresse, Youngeun Kim, Jongmin Kim and Peng Yin
A pH-Responsive DNA Walker that is Dynamically Controlled
Dongbao Yao, Sanchita Bhadra, Erhu Xiong, Haojun Liang, Andrew Ellington and Cheulhee Jung
Towards more storage for less synthesis by using composite DNA letters
Leon Anavy, Inbal Vaknin, Orna Atar, Roee Amit and Zohar Yakhini
Structure sampling for rate estimation in tethered molecular circuits
Matthew R. Lakin, Julian Weisburd and Sarika Kumar
Independent Control of the Thermodynamic and Kinetic Properties of Aptamer Switches
Brandon Wilson, Amani Hariri, Ian Thompson and Tom Soh
Development of a Single Probe Domain for Multiplexed Nucleotide Profile Recognition
Seung Won Shin, Charles Park, James J. Moon, Dan Luo and Soong Ho Um
A computational framework for DNA sequencing-based microscopy
Ian T Hoffecker, Yunshi Yang, Giulio Bernardinelli, Pekka Orponen and Björn Högberg
Live dynamical tracking of mRNA transcripts in single E. coli cells reveals bursts of fluorescence degradation
Naor Granik, Noa Katz, Yoav Shechtman and Roee Amit
A Universal Self-Replicating Computer using DNA Sticker CAM
Mark Arnold and Israel Martinez-Perez
Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols
David Doty and Mahsa Eftekhari Hesari
General-purpose analysis package for coarse-grained simulations of DNA/RNA nanotechnology
Erik Poppleton, Michael Matthies, Shuchi Sharma, Joakim Bohlin and Petr Sulc
Transduction and Processing of Protease Activity Using DNA
Hieu Bui, Mario Ancona, Ellen Goldman, Yongchan Kim, Divita Mathur and Igor Medintz
Design automation for DNA origami mechanisms
Chao-Min Huang, Anjelica Kucinic, Carlos Castro and Hai-Jun Su
Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks
Drew Lysne, Timothy Hachigian, Kailee Jones, Alma Stosius, Jeunghoon Lee and Elton Graugnard
Molecular tagging with nanopore-orthogonal DNA strands
Katie Doroschak, Karen Zhang, Aishwarya Mandyam, Melissa Queen, Karin Strauss, Luis Ceze and Jeff Nivala
Composable computation in discrete chemical reaction networks
Eric Severson, David Haley and David Doty
Nanopore readout for scalable DNA circuit reporting
Karen Zhang, Yuan-Jyue Chen, Katie Doroschak, Karin Strauss, Luis Ceze and Jeff Nivala
SOLQC: Synthetic Oligo Library Quality Control Tool
Omer Sabary, Yoav Orlev, Roy Shafir, Leon Anavy, Eitan Yaakobi and Zohar Yakhini
Super-resolution imaging of single proteins in molecular complexes in cells with small labelling probes and programmable DNA molecules
Thomas Schlichthaerle, Ralf Jungmann, Maximilian T. Strauss, Florian Schueder, Alexandra Eklund, Alexander Auer, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jervis Thevathasan, Jonas Ries, Christian Tiede, Michelle Peckham, Alistair Curd and Jan Ellenberg
pH responsive DNA origami lipid nanopore
Jasleen Kaur Daljit Singh, Natalie Surace, Joel Hochstetter, Eric Jenner, Charlotte Haunton, Claudia Leung, Ravi Jaiswar, Michael Liu, Zhenxu Yang, Minh Tri Luu, Ali Abbas and Shelley Wickham
Reversible Models for Programming Molecular Computers
William Earley
Performance Trade-offs in Reversible Amorphous Computers
William Earley
Cumulative deformation of a linear DNA origami nanoarm designed by module-based approaches
Kohei Mizuno, Yuki Suzuki, Ibuki Kawamata and Satoshi Murata

Tuesday Session

DNA nanostructures from double-C-shaped motifs with controllable angles, twist and curvature
Kai Huang, Donglei Yang, Zhenyu Tan, Silian Chen, Pengfei Wang, Ye Xiang, Yongli Mi, Chengde Mao and Bryan Wei
Possibility and impossibility in DNA strand displacement
Robert F. Johnson and Lulu Qian
Designing switchable Cas12a guide RNAs
Lukas Oesinghaus and Friedrich Simmel
Conformational isomerization of DNA nanostructures based on enzymatic treatment
Qi Yan, Yaqi Wang and Bryan Wei
Construction of DNA Amplification Circuit for Directing DNA Nanodevices and Quantifying Nucleic Acids
Ken Komiya, Teruya Enomoto and Masayuki Yamamura
Angle Control of 2D Tessellation Patterns by Simple Junction Motifs
Wen Wang, Tianqing Zhang, Chunyu Chen, Chengxian Wu and Bryan Wei
Automated Design of Scaffold-free Wireframe DNA Nanostructures
Abdulmelik Mohammed, Wen Wang, Bryan Wei and Pekka Orponen
DNA origami nanostructures with scaffolds obtained from rolling circle amplification
Mengyuan Xu, Chi Zhang, Cunjun Zhang and Bryan Wei
Programmable nucleation of 1D DNA nanostructures with DNA slats
Dionis Minev, William Shih, Chris Wintersinger, Richard Guerra and Anastasia Ershova
Controlled Nucleation of DNA Origami Megastructures using Crisscross Cooperativity
Chris Wintersinger, Dionis Minev, Jonathan F. Berengut and William M. Shih
Probing the Physical Limits of Reliable DNA Data Retrieval
Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Karin Strauss and Luis Ceze
Triangular DNA origami nanostructure having multiple self-assembly modes
Yuki Takeda, Yuki Suzuki and Satoshi Murata
Dynamics and computation of switchable DNA nanostructures based on toehold-free strand displacement
Hong Kang, Tong Lin, Xiaojin Xu, Qingshan Jia, Richard Lakerveld and Bryan Wei
Binarized Neural Networks as Droplet-Mediated Strand Displacement Cascades
Johannes Linder, David Wong, Yuan-Jyue Chen, Luis Ceze, Georg Seelig and Karin Strauss
ALCH: An Imperative Language for the Chemical Reaction Network-Controlled Tile Assembly Model
Titus Klinge, James Lathrop, Sonia Moreno, Hugh Potter, Narun Raman and Matthew Riley
Simulation of Tethered One-Legged Molecular Walkers on Independent 1-D Tracks
David Arredondo and Darko Stefanovic
Reservoir Computing for Genome Sequence Classification
Christopher Neighbor and Adan Myers Y Gutierrez
Diagonal-cut square-lattice DNA origami
Luzia Kilwing, Bhavik Nathwani, Richard Guerra, Tim Liedl and William Shih
Efficient Approximation of Sequence Hybridization
Thomas Heinis and David Buterez
Encoding Information in Primers
Thomas Heinis and Jeremy Ling
A database of cadnano file to store design information of DNA nanostructure
Ibuki Kawamata, Sho Aradachi and Satoshi Murata
Boolean Circuits via Thermodynamic Binding Networks: From Theory to Test Tube
Boya Wang, Cameron Chalk and David Soloveichik
Design of controlled promiscuous DNA interaction networks
Joseph Berleant, Kristin Sheridan and Mark Bathe
Quantifying effects of small changes on DNA origami nanotubes using a coarse-grained model
Domen Presern and Jonathan P. K. Doye
Modeling nucleation for self-assembled structures with uneven concentrations
Jackson O'Brien, Constantine Evans, Erik Winfree and Arvind Murugan
Reservoir Computing with Random DNA Strand Displacement Circuit Systems
Hoang Nguyen, Peter Banda, Darko Stefanovic and Christof Teuscher
Using Variational AutoEncoders for exploring molecular reaction networks behavior space
Erika Yamazaki and Nathanael Aubert-Kato
Combinatoric Catalytic Reaction Networks
William Poole
Counting with thermodynamic binding networks
David Haley, Eric E Severson and David Doty
Multidimensional Data Organization and Random Access in DNA Storage Systems
Xin Song, Shalin Shah and John Reif