Volume
LIPIcs, Volume 314
30th International Conference on DNA Computing and Molecular Programming (DNA 30)
Event
DNA 30, September 16-20, 2024, Baltimore, Maryland, USAEditors
Publication Details
- published at: 2024-09-09
- Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
- ISBN: 978-3-95977-344-7
- DBLP: db/conf/dna/dna2024
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Document
Complete Volume
LIPIcs, Volume 314, DNA 30, Complete Volume
Abstract
LIPIcs, Volume 314, DNA 30, Complete Volume
Cite as
30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1-124, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@Proceedings{seki_et_al:LIPIcs.DNA.30,
title = {{LIPIcs, Volume 314, DNA 30, Complete Volume}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {1--124},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30},
URN = {urn:nbn:de:0030-drops-209272},
doi = {10.4230/LIPIcs.DNA.30},
annote = {Keywords: LIPIcs, Volume 314, DNA 30, Complete Volume}
}
Document
Front Matter
Front Matter, Table of Contents, Preface, Conference Organization
Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as
30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{seki_et_al:LIPIcs.DNA.30.0,
author = {Seki, Shinnosuke and Stewart, Jaimie Marie},
title = {{Front Matter, Table of Contents, Preface, Conference Organization}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {0:i--0:xiv},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.0},
URN = {urn:nbn:de:0030-drops-209284},
doi = {10.4230/LIPIcs.DNA.30.0},
annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks
Abstract
Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. Their practical advantages include speed and scalability of interactions between components tethered near to each other on an underlying nanostructure, and the ability to restrict interactions between more distant components. The latter is a critical feature that must be factored into computational tools for the design and simulation of localized molecular devices: unlike in solution-phase systems, the geometries of molecular interactions must be accounted for when attempting to determine the network of possible reactions in a tethered molecular system. This work aims to address that challenge by integrating, for the first time, automated approaches to analysis of molecular geometry with reaction enumeration algorithms for DNA strand displacement reaction networks that can be applied to tethered molecular systems. By adapting a simple approach to solving the biophysical constraints inherent in molecular interactions to be applicable to tethered systems, we produce a localized reaction enumeration system that enhances previous approaches to reaction enumeration in tethered system by not requiring users to explicitly specify the subsets of components that are capable of interacting. This greatly simplifies the user’s task and could also be used as the basis of future systems for automated placement or routing of signal-transmission and logical processing in molecular devices. We apply this system to several published example systems from the literature, including both tethered molecular logic systems and molecular robots.
Cite as
Matthew R. Lakin and Sarika Kumar. Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{lakin_et_al:LIPIcs.DNA.30.1,
author = {Lakin, Matthew R. and Kumar, Sarika},
title = {{Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {1:1--1:24},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.1},
URN = {urn:nbn:de:0030-drops-209294},
doi = {10.4230/LIPIcs.DNA.30.1},
annote = {Keywords: Localized circuits, reaction enumeration, DNA strand displacement, geometry, molecular computing}
}
Document
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds
Abstract
Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits.
Cite as
Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods. Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 2:1-2:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{demaine_et_al:LIPIcs.DNA.30.2,
author = {Demaine, Erik D. and Gomez, Timothy and Grizzell, Elise and Hecher, Markus and Lynch, Jayson and Schweller, Robert and Shalaby, Ahmed and Woods, Damien},
title = {{Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {2:1--2:24},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.2},
URN = {urn:nbn:de:0030-drops-209304},
doi = {10.4230/LIPIcs.DNA.30.2},
annote = {Keywords: Domain-based DNA designs, minimum free energy, efficient algorithms, NP-hard, P-hard, NC, fixed-parameter tractable}
}
Document
Simulation of the Abstract Tile Assembly Model Using Crisscross Slats
Abstract
The abstract Tile Assembly Model (aTAM) provides an excellent foundation for the mathematical study of DNA-tile-based self-assembling systems, especially those wherein logic is embedded within the designs of the tiles so that they follow prescribed algorithms. While such algorithmic self-assembling systems are theoretically powerful, being computationally universal and capable of building complex shapes using information-theoretically optimal numbers of tiles, physical DNA-based implementations of these systems still encounter formidable error rates and undesired nucleation that hinder this theoretical potential. Slat-based self-assembly is a recent development wherein DNA forms long slats that combine together in 2 layers, rather than square tiles in a plane. In this approach, the length of the slats is key; while tiles typically only bind to 2 neighboring tiles at a time, slats may bind to dozens of other slats. This increased coordination between slats means that several mismatched slats must coincidentally meet in just the right way for errors to persist, unlike tiles where only a few are required. Consequently, while still a novel technology, large slat-based DNA constructions have been successfully implemented in the lab with resilience to many tile-based construction problems. These improved error characteristics come at a cost however, as slat-based systems are often more difficult to design and simulate than tile-based ones. Moreover, it has not been clear whether slats, with their larger sizes and different geometries, have the same theoretical capabilities as tiles. In this paper, we show that slats are capable of doing anything that tiles can, at least at scale. We demonstrate that any aTAM system may be converted to and simulated by an effectively equivalent system of slats. Furthermore, we show that these simulating slat systems can be made more efficiently, using shorter slats and a smaller scale factor, if the simulated tile system avoids certain uncommon growth patterns. Specifically, we consider 5 classes of aTAM systems with increasing complexity, from zig-zag systems which grow in a rigid pattern to the full class of all aTAM systems, and show how they may be converted to equivalent slat systems. We show that the simplest class may be simulated by slats at only a 2c × 2c scale, where c is the freely chosen coordination number of the slats, and further show that the full class of aTAM systems can be simulated at only a 5c × 5c scale. These results prove that slats have the full theoretical power of aTAM tiles while also providing constructions that are compact enough for potential DNA-based implementations of slat systems that are both capable of powerful algorithmic self-assembly and possessing of the strong error resilience of slats.
Cite as
Phillip Drake, Daniel Hader, and Matthew J. Patitz. Simulation of the Abstract Tile Assembly Model Using Crisscross Slats. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 3:1-3:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{drake_et_al:LIPIcs.DNA.30.3,
author = {Drake, Phillip and Hader, Daniel and Patitz, Matthew J.},
title = {{Simulation of the Abstract Tile Assembly Model Using Crisscross Slats}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {3:1--3:25},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.3},
URN = {urn:nbn:de:0030-drops-209315},
doi = {10.4230/LIPIcs.DNA.30.3},
annote = {Keywords: DNA origami, tile-assembly, self-assembly, aTAM, kinetic modeling, computational modeling}
}
Document
Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops
Abstract
We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).
Cite as
Antti Elonen and Pekka Orponen. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{elonen_et_al:LIPIcs.DNA.30.4,
author = {Elonen, Antti and Orponen, Pekka},
title = {{Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {4:1--4:12},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.4},
URN = {urn:nbn:de:0030-drops-209325},
doi = {10.4230/LIPIcs.DNA.30.4},
annote = {Keywords: RNA origami, wireframe nanostructures, polyhedra, kissing loops, topological graph embeddings, self-assembly}
}
Document
Learning and Inference in a Lattice Model of Multicomponent Condensates
Abstract
Life is chemical intelligence. What is the source of intelligent behavior in molecular systems? Here we illustrate how, in contrast to the common belief that energy use in non-equilibrium reactions is essential, the detailed balance equilibrium properties of multicomponent liquid interactions are sufficient for sophisticated information processing. Our approach derives from the classical Boltzmann machine model for probabilistic neural networks, inheriting key principles such as representing probability distributions via quadratic energy functions, clamping input variables to infer conditional probability distributions, accommodating omnidirectional computation, and learning energy parameters via a wake phase / sleep phase algorithm that performs gradient descent on the relative entropy with respect to the target distribution. While the cubic lattice model of multicomponent liquids is standard, the behaviors exhibited by the trained molecules capture both previously-observed phenomena such as core-shell condensate architectures as well as novel phenomena such as an analog of Hopfield associative memories that perform recall by contact with a patterned surface. Our final example demonstrates equilibrium classification of MNIST digits. Experimental implementation using DNA nanostar liquids is conceptually straightforward.
Cite as
Cameron Chalk, Salvador Buse, Krishna Shrinivas, Arvind Murugan, and Erik Winfree. Learning and Inference in a Lattice Model of Multicomponent Condensates. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 5:1-5:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
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@InProceedings{chalk_et_al:LIPIcs.DNA.30.5,
author = {Chalk, Cameron and Buse, Salvador and Shrinivas, Krishna and Murugan, Arvind and Winfree, Erik},
title = {{Learning and Inference in a Lattice Model of Multicomponent Condensates}},
booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
pages = {5:1--5:24},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-344-7},
ISSN = {1868-8969},
year = {2024},
volume = {314},
editor = {Seki, Shinnosuke and Stewart, Jaimie Marie},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.5},
URN = {urn:nbn:de:0030-drops-209330},
doi = {10.4230/LIPIcs.DNA.30.5},
annote = {Keywords: multicomponent liquid, Boltzmann machine, phase separation}
}