Tentative Program
TUTORIAL
| Monday June 2, 2008 | |
|---|---|
| 08:30 − 09:00 | Tutorial Registration |
| 09:00 − 09:05 | Tutorial Opening |
| 09:05 − 10:35 | Molecular Biology for (not only) Computer Scientists
Friedrich Simmel |
| 10:35 − 11:00 | Coffee break |
| 11:00 − 12:30 | Structural DNA Nanotechnology
Ned Seeman |
| 12:30 − 14:00 | Lunch break |
| 14:00 − 15:30 | Formal Grammars for DNA-Computation and Bioinformatics
Yasubumi Sakakibara |
| 15:00 − 20:00 | DNA 14 Meeting Registration |
| 16:00 − 19:00 | Guided Walking Tour |
DNA 14 MEETING
| Tuesday June 3, 2008 | |
|---|---|
| 08:30 − 18:00 | DNA 14 Meeting Registration |
| 09:00 − 09:05 | Opening |
| 09:05 − 10:00 | Plenary Talk |
| Molecules as Automata
Luca Cardelli | |
| 10:00 − 10:50 | Session T1, Chair: Yasubumi Sakakibara |
| 10:00 − 10:25 | Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation
J. Reif and U. Majumder |
| 10:25 − 10:50 | Algorithm of Myogenic Development
E. Keinan , R. Piran, E. Halperin, N. Guttmann-Raviv and R. Reshev |
| 10:50 − 11:10 | Coffee break |
| 11:10 − 12:25 | Session E1, Chair: Friedrich Simmel |
| 11:10 − 11:35 | Carbon Films Enable Light-Directed Synthesis of High-Density DNA Arrays on Metal Substrates
M.R. Lockett, J.B. Mandir, S.C. Weibel, M.F. Phillips, M.R. Shortreed, B.L. Frey, B. Sun, R.M. Corn, R.J. Hamers, F. Cerrina and L. Smith |
| 11:35 − 12:00 | Construction of Photons-Fuelled DNA Nanomachines by Tethering Azobenzenes as Engines
X. Liang, H. Nishioka, N. Takenaka and H. Asanuma |
| 12:00 − 12:25 | Weighted Sum Computation in Vitro Using Differentially Labeled Molecular Beacon Mixture
S. H. Lee, H.-W. Lim, K.-A. Yang, S. I. Yoo, B.-T. Zhang and T. H. Park |
| 12:25 − 14:00 | Lunch break |
| 14:00 − 15:40 | Session T2, Chair: Giancarlo Mauri |
| 14:00 − 14:25 | Sequentiality Induced by Spike Number in SNP Systems
O. Ibarra, A. Paun and A. Rodriguez-Paton |
| 14:25 − 14:50 | Connecting the Dots: Molecular Machinery for Distributed Robotics
Y. Brun and D. Reishus |
| 14:50 − 15:15 | DNA as a Universal Substrate for Chemical Kinetics
D. Soloveichik, G. Seelig and E. Winfree |
| 15:15 − 15:40 | Stochastic Dynamics in Artificial Transcriptional Feedback Networks
R. Jungmann, E. Friedrichs , A. Tsokou and F. Simmel |
| 15:40 − 16:00 | Coffee break |
| 16:00 − 17:40 | Session E2, Chair: John Reif |
| 16:00 − 16:25 | Experimental Validation of Signal Dependent Operation in Whiplash PCR
K. Komiya, M. Yamamura and J. Rose |
| 16:25 − 16:50 | Operon Structure Optimization by Random Self-Assembly
Y. Nakagawa, K. Yugi, K. Tsuge, M. Itaya, H. Yanagawa and Y. Sakakibara |
| 16:50 − 17:15 | Symmetric Self-Assembling DNA Nanostructures and Metallized Six-Helix Bundles
T. Liedl and W. Shih |
| 17:15 − 17:40 | Stochastic Simulation of Multivalent Random Walkers
M. Olah, M. Stojanovic and D. Stefanovic |
| 19:00 | Meeting Point for Welcome Reception |
| 19:30 | Welcome Reception in Michna Palace |
| Wednesday June 4, 2008 | |
| 09:00 − 10:00 | Plenary Talk |
| Molecular Choreography - Programming Nucleic Acid Self-Assembly and Disassembly Pathways
Niles Pierce | |
| 10:00 − 10:50 | Session T3, Chair: Satoshi Kobayashi |
| 10:00 − 10:25 | Self-Assembly of Discrete Self-Similar Fractals
M. Patitz and S. Summers |
| 10:25 − 10:50 | Time Optimal Self-Assembly of 2D and 3D Shapes: the Case of Squares and Cubes
F. Becker, E. Remila and N. Schabanel |
| 10:50 − 11:10 | Coffee break |
| 11:10 − 12:25 | Session E3, Chair: Erik Winfree |
| 11:10 − 11:35 | Programmable Transducer by DNA Self-assembly
B. Chakraborty, N. Jonoska and N.C. Seeman |
| 11:35 − 12:00 | Tiamat: a Three-Dimensional Editing Tool for Complex DNA Structures
S. Williams, P. Wonka, K. Lund, Ch. Lin, S. Lindsay and H. Yan |
| 12:00 − 12:25 | Towards DNA Comparator: the Machine that Compares DNA Concentrations
F. Tanaka, T. Tsuda and M. Hagiya |
| 12:25 − 14:00 | Lunch break |
| 14:00 − 15:00 | Plenary Talk |
| RNA-Guided, Epigenetic Programming and Re-Programming of Genomic Information in Ciliates
Laura Landweber | |
| 15:00 − 15:50 | Session E4, Chair: Masami Hagiya |
| 15:00 − 15:25 | Capture and Release of Protein by a Reversible DNA-Induced Sol-Gel
Y. Mi, B. Wei, I. Cheng and K. Luo |
| 15:25 − 15:50 | Dynamic Allosteric Control of Non-Covalent DNA Catalysis Reactions
D. Zhang and E. Winfree |
| 15:50 − 16:10 | Coffee break |
| 16:10 − 17:25 | Session T4, Chair: Natasha Jonoska |
| 16:10 − 16:35 | A Software Tool for Analyzing Combinatorial Hybridization Reaction Systems
S. Kobayashi |
| 16:35 − 17:00 | Robust Self-Assembly in Graphs
S. Angelov, S. Khanna and M. Visontai |
| 17:00 − 17:25 | A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits
L. Qian and E. Winfree |
| 17:25 − 18:30 | Poster Session |
Poster SessionDNA Sequence Set Design Based on DNA Multiplex Hybridization ReactionsE. Arai , F. Tanaka and M. Hagiya Reducing Tileset Size: 3-SAT and Beyond Y. Brun Self-Assembly of Carbon Nanotubes Devices by Bio-Directed Approach A. Filoramo, K. Nguyen, C.-L. Chung, S. Lyonnais , M. Monteverde, S. Campidelli, L. Goux-Capes, M. Goffman and J.-P. Bourgoin Synthetic Nicking Reaction for a Programmed Walk by a Multi-Legged DNA Walking Device M. Fujita, K. Komiya and M. Yamamura Chemical Modification of Azobenzene for Efficient Photoregulation of DNA Hybridization N. Hidenori, X. Liang and H. Asanuma A Proposal to a Generalised Splicing with a Self Assembly Approach L. Jeganathan, R.a Raghavan and R. Sengupta A DNA-Based Solution to the SAT Problem Using Adleman-Lipton Model with Stickers J. Liu and K. Li The Phenomenon of Sampling and Growing in Bio-Populations V. Manca, G. Franco, S. Lampis and G. Vallini A Theoretical Biomolecular Turing Machine Based on Sticker Model and Restriction Enzymes I. Marti and L.A. Garcia UNIQUIMER 3D, a Software for Structural DNA Nanotechnology Design, Analysis and Evaluation Y. Mi, J. Zhu, Y. Yuan and B. Wei Hamming Codes in the Context of DNA Self Assembly A. Mittal, T. Wang and K. Hymes Towards Photo-Controllable Self-Assembly of DNA Tiles A. Nishikawa, K. Ohtake, F. Tanaka and M. Hagiya Stepwise State-Transition of DNA Structures Controlled through Sequential Photonic Signals Y. Ogura, Y. Horiguchi and J. Tanida Toward Decoding Arrays Using Parallel Bio-Molecular Computation Monitored by SPR T. Ratner, R. Piran and E. Keinan SNP Pattern Matching by DNA Computing Y. Sakai, T. Nakajima and A. Suyama Sticker Expressions J.M. Sempere Image Encryption and Deciphering using Bio-Molecular Computing Devices S. Shoshani, R. Piran, Y. Arava and E. Keinan DNA Computing Solve the 3-SAT Problem with a Small Solution Space X. Wang A Universal DNA Computer Based on Ligase Chain Reaction X. Wang Constructing RNAi-Based NOR Gates for Cellular Programming K.-A. Yang, J. Lee and B.-T. Zhang In Vitro Proteosynthesis Molecular Automaton Based on RTRACS L. Young-Hun, S. Koh-ichiroh, K. Daisuke and A. Suyama | |
| Thursday June 5, 2008 | |
| 09:00 − 10:00 | Plenary Talk |
| Modern Homology Search
Ming Li | |
| 10:00 − 10:50 | Session T5, Chair: Lila Kari |
| 10:00 − 10:25 | Polyomino-Safe DNA Self-Assembly Via Block Replacement
C. Luhrs |
| 10:25 − 10:50 | Speeding Up Local-Search Type Algorithms for Designing DNA Sequences under Thermodynamical Constraints
S. Kawashimo , Y.K. Ng, H. Ono, K. Sadakane and M. Yamashita |
| 10:50 − 11:10 | Coffee break |
| 11:10 − 12:10 | General Assembly Meeting, Closing |
| 12:10 − 13:30 | Steering Committee Meeting |
| 12:10 − 14:00 | Lunch break |
| 14:30 − 22:00 | Excursion & Conference Dinner |
NANODAY
| Friday June 6, 2008 | |
|---|---|
| 09:00 − 09:05 | Opening |
| 09:05 − 10:35 | Adding Functionality to DNA Arrays. The Development of Semisynthetic DNA-Protein Conjugates
Christof Niemeyer |
| 10:35 − 11:00 | Coffee break |
| 11:00 − 12:30 | Formation of Nanostructures by DNA-Programmed Assembly and Conjugate Coupling
Kurt Vesterager Gothelf |
| 12:30 − 14:00 | Lunch break |
| 14:00 − 15:30 | DNA Computation
Andrew Ellington |
| 15:30 − 15:50 | Coffee break |
| 15:50 − 17:20 | Toward Self-Replicating Colloids
Using Sticky DNA
David Pine |
