DNA Computing and Molecular Programming

1. Front Matter

   Pages I-XII

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2. Automated, Constraint-Based Analysis of Tethered DNA Nanostructures

   • Matthew R. Lakin, Andrew Phillips

   Pages 1-16

3. DNA-Templated Synthesis Optimization

   • Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk

   Pages 17-32

4. Ruleset Optimization on Isomorphic Oritatami Systems

   • Yo-Sub Han, Hwee Kim

   Pages 33-45

5. Unknotted Strand Routings of Triangulated Meshes

   • Abdulmelik Mohammed, Mustafa Hajij

   Pages 46-63

6. The Design Space of Strand Displacement Cascades with Toehold-Size Clamps

   • Boya Wang, Chris Thachuk, Andrew D. Ellington, David Soloveichik

   Pages 64-81

7. A Stochastic Molecular Scheme for an Artificial Cell to Infer Its Environment from Partial Observations

   • Muppirala Viswa Virinchi, Abhishek Behera, Manoj Gopalkrishnan

   Pages 82-97

8. Complexities for High-Temperature Two-Handed Tile Self-assembly

   • Robert Schweller, Andrew Winslow, Tim Wylie

   Pages 98-109

9. A DNA Neural Network Constructed from Molecular Variable Gain Amplifiers

   • Sherry Xi Chen, Georg Seelig

   Pages 110-121

10. A Stochastic Approach to Shortcut Bridging in Programmable Matter

    • Marta Andrés Arroyo, Sarah Cannon, Joshua J. Daymude, Dana Randall, Andréa W. Richa

    Pages 122-138

11. A Minimal Requirement for Self-assembly of Lines in Polylogarithmic Time

    • Yen-Ru Chin, Jui-Ting Tsai, Ho-Lin Chen

    Pages 139-154

12. Robust Detection in Leak-Prone Population Protocols

    • Dan Alistarh, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik, Przemysław Uznański

    Pages 155-171

13. Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates

    • Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt et al.

    Pages 172-187

14. Simplifying Analyses of Chemical Reaction Networks for Approximate Majority

    • Anne Condon, Monir Hajiaghayi, David Kirkpatrick, Ján Maňuch

    Pages 188-209

15. Chemical Boltzmann Machines

    • William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree et al.

    Pages 210-231

16. A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities

    • Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree

    Pages 232-248

17. Thermodynamic Binding Networks

    • David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods

    Pages 249-266

18. Back Matter

    Pages 267-267

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This book constitutes the refereed proceedings of the 23th International Conference on DNA Computing and Molecular Programming, DNA 23, held Austin, TX, USA, in September 2017. The 16 full papers presented were carefully selected from 23 submissions. Research in DNA computing aims to draw together mathematics, computerscience, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. The papers address all areas related to biomolecular computing such as: algorithms and models for computation with biomolecular systems; computational processes in vitro and in vivo; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine.

 

• DNA Computing
• molecular programming
• self assembly
• chemical reaction networks
• population protocols
• formal verification
• programmable matter
• neural networks
• DNA circuits
• DNA strand displacement
• DNA nanotechnology
• DNA nanostructures
• DNA origami
• thermodynamics
• kinetics
• stochasticity
• algorithm analysis and problem complexity
• data structures

• Hasselt University, Diepenbeek, Belgium

  Robert Brijder

• California Institute of Technology, Pasadena, USA

  Lulu Qian

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