Accepted Papers for Track A – Full Paper

  • Matthew R. Lakin and Andrew Phillips. Automated, constraint-based analysis of tethered DNA nanostructures
  • Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle and Alexei Mihalchuk. DNA-Templated Synthesis Optimization
  • Yo-Sub Han and Hwee Kim. Ruleset Optimization on Isomorphic Oritatami Systems
  • Abdulmelik Mohammed and Mustafa Hajij. Unknotted Strand Routings of Triangulated Meshes
  • Boya Wang, Chris Thachuk, Andrew Ellington and David Soloveichik. The design space of strand displacement cascades with toehold-size clamps
  • Muppirala Viswa Virinchi, Abhishek Behera and Manoj Gopalkrishnan. A stochastic molecular scheme for an artifical cell to infer its environment from partial observations
  • Robert Schweller, Andrew Winslow and Tim Wylie. Complexities for High-Temperature Two-Handed Tile Self-Assembly
  • Sherry Xi Chen and Georg Seelig. A DNA neural network constructed from molecular variable gain amplifiers
  • Marta Andrés Arroyo, Sarah Cannon, Joshua J. Daymude, Dana Randall and Andréa W. Richa. A Stochastic Approach to Shortcut Bridging in Programmable Matter
  • Yen-Ru Chin, Jui-Ting Tsai and Ho-Lin Chen. A Minimal Requirement for Self-Assembly of Lines in Polylogarithmic Time
  • Dan Alistarh, Bartłomiej Dudek, Adrian Kosowski, Daivid Soloveichik and Przemysław Uznański. Robust Detection in Leak-Prone Population Protocols
  • Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M Schaeffer, Mark Schmidt, Chris Thachuk and Erik Winfree. Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates
  • Monir Hajiaghayi, Anne Condon, David Kirkpatrick and Jan Manuch. Simplifying Analyses of Chemical Reaction Networks for Approximate Majority
  • William Poole, Andres Ortiz-Munoz, Abhishek Behera, Nick Jones, Thomas Ouldridge, Erik Winfree and Manoj Gopalkrishnan. Chemical Boltzmann Machines
  • Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk and Erik Winfree. A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities.
  • David Doty, Trent Rogers, David Soloveichik, Chris Thachuk and Damien Woods. Thermodynamic Binding Networks

Accepted Papers for Track B – One-Page Abstract

  • Dongsheng Liu. Two-dimensional assembly of amphiphilic molecules into free-floating nanosheets with tailored size and shape
  • Jocelyn Kishi, Thomas Schaus, Nikhil Gopalkrishnan, Feng Xuan and Peng Yin. Programmable autonomous synthesis of single-stranded DNA
  • Cheulhee Jung, Peter Allen and Andrew Ellington. A simple, cleated DNA walker that hangs on to surfaces
  • Anna J Simon, Arti Pothukuchy, Jillian Gerberich, Janelle Leggere, Jimmy Golihar, Cheulhee Jung, David Taylor and Andrew Ellington. Supercharging enables tunable hierarchical assembly of synthetic proteins
  • Antoine Bader and Scott Cockroft. Enhancing the fidelity of toehold-sequestered nucleic acid devices
  • Sifang Chen and Georg Seelig. Programmable DNA pattern formation
  • Sundipta Rao, Yuan-Jyue Chen and Georg Seelig. Next generation plasmid-derived DNA gates with quantitatively controlled kinetics
  • Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin and Erik Winfree. Iterated Boolean circuit computation via a programmable DNA tile array

To access a copy of the submitted papers and abstracts please follow this link:

LNCS Volume 10467

Accepted Posters for Track C – Poster

  • Thorsten L Schmidt, Michael Matthies, Nayan Agarwal and Bastian Joffroy. Triangulated construction motifs for DNA nanotechnology
  • Thomas Schaus, Sungwook Woo, Feng Xuan, Xi Chen and Peng YinA Biochemical Nanoscope via Auto-cycling Proximity Recording
  • Akinori Kuzuya, Yuta Ikeda, Yuta Yamasaki and Yuichi Ohya. Knotting a Synthetic Polymer with DNA Helicity
  • Pierre-Étienne Meunier and Damien WoodsThe non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation
  • Azat AkhmetovAndrew Ellington and Edward MarcotteA highly parallel strategy for storage of digital information in living cells
  • Shizuma Tanaka, Kenta Wakabayashi, Kazuki Fukushima, Shinsuke Yukami, Akinori Kuzuya and Yuichi Ohya. Intelligent, Biodegradable, and Self-Healing Hydrogels Utilizing DNA Quadruplexes formation
  • Yuichi Ohya, Kazuki Fukushima, Shizuma Tanaka, Kenta Wakabayashi, Shinsuke Yukami and Akinori Kuzuya. Metal ion-responsive hydrogels using PEG-DNA copolymers
  • Shohei Kotani and William HughesMulti-Arm Junctions for Dynamic DNA Nanotechnology
  • Hossein Yazdi, Ryan Gabrys and Olgica Milenkovic. Portable and Error-Free DNA-Based Data Storage
  • Thuy Jane Dinh Nguyen, Ilenia Manuguerra, Vipin Kumar and Kurt Vesterager Gothelf. A New Mechanism for the Strand Displacement Reaction using Acyclic L-Threoninol Nucleic Acid Based Triplex Structures
  • Benjamin Aleritsch and Friedrich SimmelA CRISPRi NAND Gate
  • Cheulhee Jung and Andrew EllingtonPhosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) system and its applications
  • Aurora Fabry-Wood, Madalyn E. Fetrow, Carl W. Brown Iii, Nicholas Baker, Nadiezda Fernandez Oropeza, Andrew P. Shreve, Gabriel A. Montaño, Darko StefanovicMatthew R. Lakin and Steven W. Graves. Monitoring Fluid DNA-based Molecular Computing Reactions with Flow Cytometry
  • Petr Sulc, Ard LouisJonathan DoyeThomas Ouldridge, Christian Matek and Flavio Romano. Coarse-grained modelling of RNA
  • Franky Djutanta, Bernard Yurke and Rizal HariadiCan double-stranded DNA function as the simplest and fastest biomolecular rotary motor?
  • Sung Won Oh, Adriana Pereira, Ting Zhang and Jinglin FuBiochemical Sensing Circuit Based on DNA-Mediated Self-Assembly of Enzyme/Cofactor Nanostructures
  • Masayuki Endo, Prakash Shrestha, Sagun Jonchhe, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama and Hanbin Mao. Biophysical property of G-quadruplex caged in a confined DNA nanospace
  • Yalan Yi, Sandra Sagredo and Friedrich Simmel. Synthetic control of chromosomal replication in E.coli
  • Juan Elezgaray and Juewen Liu. Two examples of DNA controlled transport across lipid membranes
  • Divita Mathur, Susan Buckhout-White, Chanel Person, Ashley A. Chapin, Ellen R. Goldman and Igor Medintz. Coding DNA Restriction into Dynamic Nanosystems: Merging Molecular Logic with Synthetic Biology
  • Carl Brown Iii, Susan Buckhout-White, Michael Stewart, Kimihiro Susumu, Ellen Goldman and Igor Medintz. A DNA-based Protease Biosensor Using Quantum Dot Nanoscaffolds
  • Takaniro Nishimura, Yusuke Ogura and Jun Tanida. A photonic DNA processor using excitation energy transfer-based signaling
  • Lukas Oesinghaus and Friedrich Simmel. Surface versus solution assembly of RNA origami nanostructures
  • Suguru Shimomura, Takahitro Nishimura, Yusuke Ogura and Jun Tanida. Photo-induced formation of DNA hydrogel using quenchers
  • Soojin Jo, Byung Ho Lee, Hyun Ki Kim, Sung Ha Park and Moon Ki Kim. Design, Synthesis, and Validation of a DNA Foldback Intercoil Structure
  • Aurore Dupin, Berta Tinao and Friedrich C. SimmelCompartmentalization and signaling in cell-free synthetic gene circuits
  • Francesca Nicoli, Tao Zhang, Mauricio Pilo-Pais and Tim Liedl. Fluorescence emission enhancement of a single quantum dot in a DNA self-assembled plasmonic cavity
  • Ibuki Kawamata, Takuto Hosoya, Fumi Takabatake, Ken Sugawara and Satoshi Murata. Pattern transition by DNA hybridization based reaction-diffusion system in cellular lattice hydrogel
  • Xiaoping Olson, Shohei Kotani, Bernard Yurke, William Hughes and Elton GraugnardAnalysis and Reduction of Leakage in DNA Strand Displacement Systems
  • Christopher M. Green, Kelly Schutt, Noah Morris, Reza M. ZadeganWilliam Hughes, Wan Kuang and Elton GraugnardMetrology of DNA Arrays by State-Dependent Super-Resolution Microscopy
  • Yuan-Jyue Chen, Christopher Takahashi, Lee Organick, Kendall Stewart, Siena Ang, Douglas Carmean, Georg Seelig, Luis Ceze and Karin Strauss. DNA storage: quantifying molecule bias with unique molecular identifiers
  • Yusei Masuda, Shinnosuke Seki and Yuki Ubukata. Algorithmic molecular self-assembly of fractals by cotranscriptional folding
  • Mark Arnold and Israel Martinez. Sticker/Staple Algorithms for forming DNA origami nanostructures
  • Matthaeus Schwarz-Schilling, Andrea Mückl, Katrin Fischer and Friedrich C. Simmel. Switchable filamentation of Escherichia coli cells controlled by a CRISPR interference circuit
  • James Rybarski, Mashelfatema A. Saifuddin, Stephen K. Jones Jr., John Hawkins, William H. Press and Ilya J. FinkelsteinHacking NGS to reveal the molecular basis for the DNA-binding specificity of Class 2 CRISPR-Cas nucleases
  • Reza M Zadegan, Kelsey Suyehira, Simon Llewellyn, Tim Andersen and William L. Hughes. A Coding Scheme for Digital Data Storage in Nucleic Acid Memory (NAM)
  • Reza M. Zadegan, Celine Tran, Natalya Hallstrom and William L. Hughes. Chromatin Analogous Gene Expression (CAGE)
  • Kiri Choi, Nicholas Roehner, Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Raik Grunberg, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Michael Zhang, Zhen Zhang, Zach Zundel, Douglas Densmore, John Gennari, Anil Wipat, Herbert Sauro and Chris Myers. Managing the Design-Build-Test Cycle for Synthetic Biology with the Synthetic Biology Open Language
  • Parsa Nafisi, Tural Aksel, Suraj Makhija and Shawn DouglasA phage-based system for production of custom single-stranded DNA scaffolds for DNA origami applications
  • Kiri Choi, J Kyle Medley, Wilbert Copeland, Standley Gu, Madhav Murthy, Kaylene Stocking and Herbert Sauro. LibRoadRunner: High-Performance Timecourse Simulation and Model Fitting
  • Yan Cui, Mingxuan Kai, Bryan Wei, Ruipeng Chen, Yaqi Wang and Yongli Mi. Versatile DNA origami nanostructures in simplified and modular designing framework
  • Tristan Stérin and Damien WoodsOn the computational power of 6-bit iterated Boolean gate arrays
  • Clothilde Coilhac, Jonathan Bath, Andrew Turberfield and Herve Guillou. Thermodynamics of the DNA tetrahedron assembly
  • Yuki Suzuki, Ibuki Kawamata, Yuki Takeda and Satoshi Murata. Self-assembly of two-dimensional DNA origami lattices with designed geometries on lipid membranes
  • Gourab Chatterjee, Neil Dalchau, Richard Muscat, Andrew Phillips and Georg Seelig. A spatially localised architecture for fast and modular DNA computing
  • Carlo Spaccasassi, Matthew Lakin, Rasmus Petersen and Andrew PhillipsRule-based modelling of DNA Strand Displacement systems
  • Cheulhee Jung, John Hawkins, Stephen Jones Jr., Yibei Xiao, James Rybarski, Kaylee Dillard, Jeffrey Hussmann, Fatema Saifuddin, Siyuan Wang, Andrew EllingtonAilong KeWilliam Pressand Ilya FinkelsteinAdaptation of the Next Generation Sequencing Platform for Molecular Applications
  • Juan Camilo Gonzalez, Asuka Orr, Mark Sherman, Mark Wilson, Phanourios Tamamis and Lydia ConterasComputational simulations of modified RNA-protein interactions driven by experimental results.
  • Yan Cui, Jun Yan, Diming Wei and Mingxuan Kai. Hybrid Wireframe DNA Nanostructures
  • Xiaojin He, Tanxi Bai, Yaqi Wang, Donglei Yang, Ruipeng Chen, Yongli Mi and Bryan Wei. Hierarchical Assembly of 2D and 3D Structures
  • Wen Wang, Silian Chen, Tanxi Bai, Ye Xiang and Bryan Wei. Self-assembly of addressable DNA wireframe nanostructures from junction motifs
  • Kai Huang, Silian Chen, Tanxi Bai, Ye Xiang and Bryan Wei. The construction of DNA polyhedral nanostructures based on junction motifs
  • Jaewon Lee, William Shih and Seungwoo Lee. Regulating light-matter interaction by tailoring custom geometry of DNA based plasmonic metamolecule
  • Christopher Bonner, Daniel Moyer, Andrea Nguyen, Elton Graugnard and Jeunghoon LeeCatalytic Disassembly of Gold Nanoparticle Aggregates Driven by an Autocatalytic DNA Network
  • Sanchita Bhadra and Andrew Ellington. Conformation switching RNA beacons as co-transcriptional diagnostic probes
  • Franky Djutanta, Damien WoodsBernard Yurke and Rizal HariadiDNA nanotubes as fluid flow sensors for measuring hydrodynamic forces in raindrop impacts
  • Dominic Scalise, Leo Potters, Madeline Noble and Rebecca SchulmanProgramming the Sequential Release of DNA
  • Sanchita Bhadra, Andrew Ellington, Yu Jiang, Timothy Riedel, Jessica Popoola, Barrett Morrow, Miguel Saldana, Grant Hughes, Luann Scott, Holly Wichman, James Allred, Justin Hardick and Charlotte Gaydos. Sample-to-answer point-of-care diagnostics using strand exchange signal processors
  • Shaunak Kar and Andrew Ellington. Design and construction of hairpin based in vitro transcriptional switches
  • Joseph Robertson, Jacob Forstater, Joseph E. Reiner, Sergei Kalachikov, James Russo, Jingyue Ju and John J. Kasianowicz. Nanopore spectroscopy for decoding molecular information
  • Samuel Schaffter and Rebecca Schulman. An orthogonal genelet architecture for inducible state-switching of a bistable circuit
  • Amjad Chowdhury and Carlos Castro. Translating DNA Origami into the Classroom
  • Fei Zhang, Xiaodong Qi, Zhaoming Su, Shuoxing Jiang, Wah Chiu, Yan Liu and Hao Yan. Programming Highly Knotted Molecular Topologies Using Single-stranded Nucleic Acids
  • David Arredondo, Darko Stefanovic and Mark Olah. The Effect of a Tether Connecting Two Molecular Spiders on a Two-Dimensional Lattice
  • Shohei Kotani, Bernard Yurke and William HughesSequestering DNA reaction network components onto nanoparticles with bumper rods to reduce leakage
  • Ryan Gabrys and Olgica Milenkovic. Coding for Uniquely Reconstructable DNA-Based Data Storage
  • James Wagner, Shuo-Fu Yuan, Joseph Abatemarco, Maen Sarhan, Jyun-Liang Lin Lin, Leqian Liu, Adam Abate and Hal Alper. RNA-Aptamers-In-Droplets (RAPID) High Throughput Screening for Secretory Phenotypes
  • Jaeseung Hahn, Richard Guerra, Leo Chou, Rasmus Schøler Sørensen and William Shih. Extrusion of therapeutic RNAsfrom a cytosolic nanofactory
  • Andrés Ortiz-Muñoz, Daniele Cappelletti, David Anderson and Erik WinfreeThe Complexity of Distributions Generated by Stochastic Chemical Reaction Networks
  • Xun Tang, Deepak Agrawal, Colin Maxwell, Chase Beisel, Alexandra Westbrook, Julius Lucks, Ryan Marshall, Vincent Noireaux, Mary Dunlop and Elisa Franco. RNA-based PID controllers for regulation of gene expression
  • Tulsi Damase and Peter AllenMolecular Transmission of catalytic DNA walkers between microparticles
  • John Hawkins, Cheulhee Jung, Ilya Finkelstein and William PressContext-Tolerant, Error-Correcting DNA Codes
  • Fan Hong, Hao Yan and Alexander Green. De-novo-designed ultraspecific riboregulators for gene regulation in vivo and in low-cost paper-based diagnostics
  • Keenan Breik, David Soloveichik, Lakshmi Prakash, Marijn Heule and Chris Thachuk. Computing properties of binding networks
  • Richard Lease and Samuel Stimple. Fingerloops: Stem-loop Antisense Motifs that Discriminate Off-target Base-pairing Interactions with High Sensitivity

    ** Highlighted posters have been selected to give a short “breaking news” talk during the DNA23 conference.**