DNA 17
17th International Conference on
DNA Computing and Molecular Programming
California Institute of Technology
Beckman Institute
Pasadena, California, USA
September 19 - 23, 2011
17th International Conference on
DNA Computing and Molecular Programming
California Institute of Technology
Beckman Institute
Pasadena, California, USA
September 19 - 23, 2011
Final Program
Monday, Sept 19: tutorial day
| 8:30am | On-site registration opens | Beckman Institute |
| 9:00am-6:00pm [all day in parallel] | Wet Lab Tutorial: In Vitro Transcriptional Circuits
Elisa Franco, Jongmin Kim, and Josh Bishop | Beckman Institute, room 121 |
| 8:30am-10:00am | refreshments | Beckman Institute courtyard |
| 10:00am-11:30am | Tutorial #1: Theory of Algorithmic Self-Assembly with DNA Tiles
David Doty |
Beckman Institute |
| 11:30am-1:30pm | lunch on your own | |
| 1:30pm-3:00pm | Tutorial #2: The Programming Language of Chemical Kinetics, and How To Discipline Your DNA Molecules using Strand Displacement Cascades
David Soloveichik | Beckman Institute |
| 3:00pm-3:30pm | break/refreshments | Beckman Institute courtyard |
| 3:30pm-5:00pm | Tutorial #3: Specification and Control of Stochastic Biochemical Systems
Eric Klavins | Beckman Institute |
| 5:00pm | dinner on your own |
All submitted talks will be allocated 20 minutes plus 5 minutes for questions afterward.
Authors prefaced with a * are student presenters eligible for the ISNSCE best student presentation award. If you are a student presenter and your name is not marked, please email dna17@caltech.edu.
Tuesday, Sept 20
| 8:30am-9:00am | introduction and information | Beckman Institute |
| 9:00am-10:00am | plenary talk: Cooperation in an All-RNA Network
Niles Lehman (introduced by Anne Condon) | Beckman Institute |
| 10:00am-10:30am | break/refreshments | Beckman Institute courtyard |
| session 1 (session chair: Andrew Phillips) | Beckman Institute | |
| 10:30am-10:55am | Less Haste, Less Waste: On Recycling and its Limits in Strand Displacement Systems.
Anne Condon, Alan Hu, Jan Manuch and *Chris Thachuk. | Beckman Institute |
| 10:55am-11:20am | Nucleic Acid Logic Gates Made From Nicked Double-Stranded DNA.
*Yuan-Jyue Chen, Cezanne Camacho and Georg Seelig. | Beckman Institute |
| 11:20am-11:40am | break/refreshments | Beckman Institute courtyard |
| session 2 (session chair: Satoshi Murata) | Beckman Institute | |
| 11:40am-12:05pm | Multivalent Random Walkers -- A Model for Deoxyribozyme Walkers.
*Mark Olah and Darko Stefanovic. | Beckman Institute |
| 12:05pm-12:30pm | Multiple Molecular Spiders With a Single Localized Source -- the One-Dimensional Case (Extended Abstract).
*Oleg Semenov, Mark Olah and Darko Stefanovic. | Beckman Institute |
| 12:30pm-2:30pm | lunch on your own | |
| 2:30pm-3:30pm | plenary talk: The Computer Science of Molecular Programming
Jack Lutz (introduced by Natasha Jonoska) | Beckman Institute |
| 3:30pm-4:00pm | break/refreshments | Beckman Institute courtyard |
| session 3 (session chair: Jack Lutz) | Beckman Institute | |
| 4:00pm-4:25pm | One-Dimensional Staged Self-Assembly.
Erik D. Demaine, Sarah Eisenstat, Mashhood Ishaque and *Andrew Winslow. | Beckman Institute |
| 4:25pm-4:50pm | Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-Assembly.
*Tuomo Lempiäinen, Eugen Czeizler and Pekka Orponen. | Beckman Institute |
| 4:50pm-5:15pm | Exact Shapes and Turing Universality at Temperature 1 with a Single Negative Glue.
Matthew Patitz, Robert Schweller and Scott Summers. | Beckman Institute |
| 5:15pm-5:30pm | break/refreshments | Beckman Institute courtyard |
| 5:30pm-7:00pm | poster session + sangria and chips | Beckman Institute courtyard |
| 7:00pm | dinner on your own |
Wednesday, Sept 21
| 9:00am-10:00am (canceled; please arrive at 10:00am) | plenary talk: Cooperative Assembly Systems
Vincent Danos | Beckman Institute |
| 10:00am-10:30am | break/refreshments | Beckman Institute courtyard |
| session 4 (session chair: Darko Stefanovic) | Beckman Institute | |
| 10:30am-10:55am | Nucleic acid sequence design via efficient ensemble defect optimization.
*Brian Wolfe, Joseph Zadeh, Robert Dirks, Conrad Steenberg and Niles Pierce. | Beckman Institute |
| 10:55am-11:20am | Localized Hybridization Circuits.
Harish Chandran, *Nikhil Gopalkrishnan, Andrew Phillips, and John Reif. | Beckman Institute |
| 11:20am-11:40am | break/refreshments | Beckman Institute courtyard |
| session 5 (session chair: Robbie Schweller) | Beckman Institute | |
| 11:40am-12:05pm | Graph-theoretic formalization of hybridization in DNA sticker complexes.
Robert Brijder, *Joris Gillis and Jan Van Den Bussche. | Beckman Institute |
| 12:05pm-12:30pm | Autonomous resolution based on DNA strand displacement.
Inaki Sainz De Murieta, Alfonso Rodriguez-Paton and Petr Sosik. | Beckman Institute |
| 12:30pm-4:30pm | excursion (lunch available for purchase there) | Huntington Gardens |
| 4:30pm-8:00pm | dinner on your own | |
| 8:00pm-8:45pm | vision panel discussion | Beckman Institute |
| 8:45pm | poster session + beer and pretzels | Beckman Institute courtyard |
Thursday, Sept 22
| 9:00am-10:00am | plenary talk: An Autonomous DNA Nanodevice Captures pH Maps of Living Cells in Culture and in Vivo Yamuna Krishnan (introduced by Ned Seeman) | Beckman Institute |
| 10:00am-10:30am | break/refreshments | Beckman Institute courtyard |
| session 6 (session chair: Yannick Rondelez) | Beckman Institute | |
| 10:30am-10:55am | Associative toehold activation: Expanding the architecture of DNA circuits with a small structural motif.
Xi Chen. | Beckman Institute |
| 10:55am-11:20am | Amorphous Computation with a DNA-based Edge Detector.
Andrew Ellington, Xi Chen, Peter Allen and Steven Chirieleison. | Beckman Institute |
| 11:20am-11:40am | break/refreshments | Beckman Institute courtyard |
| session 7 (session chair: Milan Stojanovic) | Beckman Institute | |
| 11:40am-12:05pm | A Cell-free Expression Toolbox: from elementary gene circuits to synthetic bacteriophages.
Vincent Noireaux and Jonghyeon Shin. | Beckman Institute |
| 12:05pm-12:30pm | A toolbox to build time-responsive in vitro DNA networks.
Kevin Montagne, Raphaël Plasson, Adrien Padirac, Teruo Fujii and Yannick Rondelez. | Beckman Institute |
| 12:30pm-2:30pm | lunch on your own | |
| 2:30pm-3:30pm | plenary talk: Designer DNA Architectures for Bionanotechnology
Hao Yan (introduced by John Reif) | Beckman Institute |
| 3:30pm-4:00pm | break/refreshments | Beckman Institute courtyard |
| session 8 (session chair: Kurt Gothelf) | Beckman Institute | |
| 4:00pm-4:25pm | Theoretical Model of Substrate-Assisted Self-Assembly of DNA motif.
Shogo Hamada and Satoshi Murata. | Beckman Institute |
| 4:25pm-4:50pm | Programmable DNA-Linked Nanoparticle Building Blocks to Self-Assemble Nanostructures with Arbitrary, Anisotropic Shapes in All Dimensions.
Jin-Woo Kim, Jeong-Hwan Kim and Russell Deaton. | Beckman Institute |
| 4:50pm-5:15pm | Nanomechanical DNA Origami Devices as Single-Molecular Visual Detectors for Various Chemical/Biochemical Targets.
Akinori Kuzuya, Sakai Yusuke, Takahiro Yamazaki and Makoto Komiyama. | Beckman Institute |
| 5:15pm-5:30pm | break/refreshments | Beckman Institute courtyard |
| 5:30pm-6:30pm | poster session + wine and cheese | Beckman Institute courtyard |
| 6:30pm-6:45pm | group picture of DNA 17 attendees | Beckman Auditorium front steps (east of the posters) |
| 7:00pm-9:00pm | banquet; presentation of awards | Athenaeum |
Friday, Sept 23
| session 9 (session chair: Matt Patitz) | Beckman Institute | |
| 9:00am-9:25am | Computing maximal Kleene closures that are embeddable in a given constrained DNA language.
Stavros Konstantinidis and Nicolae Santean. | Beckman Institute |
| 9:25am-9:50am | Modelling, simulating and verifying Turing-powerful strand displacement systems.
Matthew R. Lakin and Andrew Phillips. | Beckman Institute |
| 9:50am-10:15am | An Improved DNA-Sticker Addition Algorithm and Its Application to Logarithmic Arithmetic.
Mark Arnold. | Beckman Institute |
| 10:15am-10:45am | break/refreshments | Beckman Institute courtyard |
| session 10 (session chair: Andy Ellington) | Beckman Institute | |
| 10:45am-11:10am | Hybridization Kinetics of Higher-Order DNA Assemblies.
Andre Vidal Pinheiro, Jeanette Nangreave, Hao Yan and Yan Liu. | Beckman Institute |
| 11:10am-11:35am | Optimizing Nucleic Acid Hybridization Specificity.
David Zhang, Sherry Xi Chen and Peng Yin. | Beckman Institute |
| 11:35am-1:30am | lunch on your own | |
| 1:30pm-2:15pm | Hard Problems Panel | Beckman Institute |
| 2:15pm-3:00pm | Applications Panel | Beckman Institute |
| 3:00pm-3:45pm | Interfaces Panel | Beckman Institute |
| 1:30pm-4:30pm | impromptu sessions | Beckman Institute and Baxter Hall (see Impromptu Sessions) |
| 4:30pm-5:00pm | adjourn |