19 Search Results for "Ouldridge, Thomas E."

Volume

LIPIcs, Volume 238

28th International Conference on DNA Computing and Molecular Programming (DNA 28)

DNA 28, August 8-12, 2022, University of New Mexico, Albuquerque, New Mexico, USA

Editors: Thomas E. Ouldridge and Shelley F. J. Wickham

Document
DOI: 10.4230/LIPIcs.DISC.2025.7
On the Shape Containment Problem Within the Amoebot Model with Reconfigurable Circuits

Authors: Matthias Artmann, Andreas Padalkin, and Christian Scheideler

Published in: LIPIcs, Volume 356, 39th International Symposium on Distributed Computing (DISC 2025)

Abstract
In programmable matter, we consider a large number of tiny, primitive computational entities called particles that run distributed algorithms to control global properties of the particle structure. Shape formation problems, where the particles have to reorganize themselves into a desired shape using basic movement abilities, are particularly interesting. In the related shape containment problem, the particles are given the description of a shape S and have to find maximally scaled representations of S within the initial configuration, without movements. For example, if S is a triangle, they have to identify the largest subsets of particles that already form a triangle. While the shape formation problem is being studied extensively, no attention has been given to the shape containment problem, which may have additional uses besides shape formation, such as detecting structural flaws. In this paper, we consider the shape containment problem within the geometric amoebot model for programmable matter, using its reconfigurable circuit extension to enable the instantaneous transmission of primitive signals on connected subsets of particles. We first prove a lower runtime bound of Ω (√n) synchronous rounds for the general problem, where n is the number of particles. Then, we present simple and efficient primitives for identifying subsets that form the desired shape. Using these primitives, we construct a large class of shapes which we call snowflakes. This class contains, among others, all shapes composed of parallelograms and hexagons, and the class of star convex shapes. Let k be the maximum scale of the considered shape in a given amoebot structure. If the shape is star convex, we solve it within 𝒪 (log² k) rounds. If it is a snowflake but not star convex, we solve it within 𝒪 (√n log n) rounds.
Cite as

Matthias Artmann, Andreas Padalkin, and Christian Scheideler. On the Shape Containment Problem Within the Amoebot Model with Reconfigurable Circuits. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 7:1-7:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{artmann_et_al:LIPIcs.DISC.2025.7,
  author =	{Artmann, Matthias and Padalkin, Andreas and Scheideler, Christian},
  title =	{{On the Shape Containment Problem Within the Amoebot Model with Reconfigurable Circuits}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{7:1--7:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-402-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{356},
  editor =	{Kowalski, Dariusz R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2025.7},
  URN =		{urn:nbn:de:0030-drops-248240},
  doi =		{10.4230/LIPIcs.DISC.2025.7},
  annote =	{Keywords: Programmable matter, amoebot model, reconfigurable circuits, shape containment}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.2
A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs

Authors: Hope Amber Johnson and Anne Condon

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
DNA strand displacement, a collective name for certain behaviors of short strands of DNA, has been used to build many interesting molecular devices over the past few decades. Among those devices are general implementation schemes for Chemical Reaction Networks, suggesting a place in an abstraction hierarchy for complex molecular programming. However, the possibilities of DNA strand displacement are far from fully explored. On a theoretical level, most DNA strand displacement systems are built out of a few simple motifs, with the space of possible motifs otherwise unexplored. On a practical level, the desire for general, large-scale DNA strand displacement systems is not fulfilled. Those systems that are scalable are not general, and those that are general don't scale up well. We have recently been exploring the space of possibilities for DNA strand displacement systems where all input complexes are made out of at most two strands of DNA. As a test case, we've had an open question of whether such systems can implement general Chemical Reaction Networks, in a way that has a certain set of other desirable properties - reversible, systematic, O(1) toeholds, bimolecular reactions, and correct according to CRN bisimulation - that the state-of-the-art implementations with more than 2-stranded inputs have. Until now we've had a few results that have all but one of those desirable properties, including one based on a novel mechanism we called coupled reconfiguration, but that depended on the physically questionable assumption that pseudoknots cannot occur. We wondered whether the same type of mechanism could be done in a pseudoknot-robust way. In this work we show that in fact, coupled reconfiguration can be done in a pseudoknot-robust way, and this mechanism can implement general Chemical Reaction Networks with all inputs being single strands of DNA. Going further, the same motifs used in this mechanism can implement stacks and surface-based bimolecular reactions. Those have been previously studied as part of polymer extensions of the Chemical Reaction Network model, and on an abstract model level, the resulting extensions are Turing-complete in ways the base Chemical Reaction Network model is not. Our mechanisms are significantly different from previously tested DNA strand displacement systems, which raises questions about their ability to be implemented experimentally, but we have some reasons to believe the challenges are solvable. So we present the pseudoknot-robust coupled reconfiguration mechanism and its use for general Chemical Reaction Network implementations; we present the extensions of the mechanism to stack and surface reactions; and we discuss the possible obstacles and solutions to experimental implementation, as well as the theoretical implications of this mechanism.
Cite as

Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{johnson_et_al:LIPIcs.DNA.31.2,
  author =	{Johnson, Hope Amber and Condon, Anne},
  title =	{{A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{2:1--2:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.2},
  URN =		{urn:nbn:de:0030-drops-238514},
  doi =		{10.4230/LIPIcs.DNA.31.2},
  annote =	{Keywords: Molecular programming, DNA strand displacement, Chemical Reaction Networks}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.7
Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics

Authors: Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
A fundamental problem in crystallisation, and in molecular tile-based self-assembly in particular, is how to simultaneously control its two main constituent processes: seeded growth and spontaneous nucleation. Often, we desire out-of-equilibrium growth without spontaneous nucleation, which can be achieved through careful calibration of temperature, concentration and experimental time-scale a laborious and overly-sensitive approach. Another technique is to find alternative nucleation-resistant tile designs [Minev et al, 2001]. Rogers, Evans and Woods [In prep] propose blockers: short DNA strands designed to dynamically block DNA tile sides, altering self-assembly dynamics. Experiments showed independent and tunable control on nucleation and growth rates. Here, we provide a theoretical explanation for these surprising results. We formally define the kBlock model where blockers bind to tiles at thermodynamic equilibrium in solution and stochastic kinetics allow self-assembly of a tiled structure. In an intentionally simplified mathematical setting we show that blockers permit reasonable seeded growth rates, akin to a non-blocked tile system at lower tile concentration, crucially giving nucleation rates that are exponentially suppressed. We then implement the kBlock model in a stochastic simulator, with results showing remarkable alignment with oversimplified theory. We provide evidence of blocker-induced tile buffering, where a large reservoir of blocked tiles slowly feeds a small unblocked tile subpopulation which acts like a regular, non-blocked, low tile concentration system, yet is capable of long-term buffered assembly. Finally, and perhaps most satisfyingly, theory and simulations align remarkably well with DNA self-assembly experiments over a wide range of concentrations and temperatures, matching the size of growth temperature windows to within 12%. Blockers are a straightforward solution to the challenging problem of simultaneously and independently controlling growth and nucleation, using a motif compatible with many DNA tile systems.
Cite as

Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods. Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{evans_et_al:LIPIcs.DNA.31.7,
  author =	{Evans, Constantine G. and Cervera Roldan, Angel and Rogers, Trent and Woods, Damien},
  title =	{{Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{7:1--7:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.7},
  URN =		{urn:nbn:de:0030-drops-238564},
  doi =		{10.4230/LIPIcs.DNA.31.7},
  annote =	{Keywords: Self-assembly, kinetic model, kinetic simulation, thermodynamic prediction}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.11
Leakless Polymerase-Dependent Strand Displacement Systems

Authors: Zoë Evelyn Mōhalakealoha Derauf and Chris Thachuk

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
A grand challenge facing molecular programmers is the rational development of fast, robust, and isothermal architectures akin to "chemical central processing units" that can sense (bio-)chemical signals from their environment, perform complex computation, and orchestrate a physical response in situ. DNA strand displacement systems (DSDs) remain a compelling candidate, but are hampered by spurious reaction pathways that lead to incorrect output. DSDs that utilize the systematic leakless motif can be made arbitrarily robust at the cost of increasing redundancy and network size (scaling), and thus a degradation of kinetic performance. Another class of architectures utilize DNA hybridization, extension, and signal production of entirely sequestered outputs via strand-displacing polymerases (SDPs) that have resulted in impressive demonstrations; however, they face similar challenges of aberrant behavior such as mis-priming by incorrect signals. Our work introduces a unified polymerase-dependent toehold-mediated strand displacement (PD-TMSD) architecture that integrates the programmed specificity of DSDs with the unique advantages of SDPs. This unification enables systems that can be made arbitrarily robust, at any concentration range, without increasing network size. We propose a number of gate designs and composition rules to compute arbitrary Boolean functions, emulate arbitrary chemical reaction networks, and explore time-bounded probabilistic computation made possible by certain classes of SDPs. Our theoretical exploration is backed by preliminary experimental demonstrations. This contribution was inspired by the belief that molecular programming can meet or exceed the complexity exhibited in biology if we embrace its best understood molecular machinery and couple it with systematic design principles built upon a strong theoretical foundation.
Cite as

Zoë Evelyn Mōhalakealoha Derauf and Chris Thachuk. Leakless Polymerase-Dependent Strand Displacement Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 11:1-11:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{derauf_et_al:LIPIcs.DNA.31.11,
  author =	{Derauf, Zo\"{e} Evelyn M\={o}halakealoha and Thachuk, Chris},
  title =	{{Leakless Polymerase-Dependent Strand Displacement Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{11:1--11:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.11},
  URN =		{urn:nbn:de:0030-drops-238608},
  doi =		{10.4230/LIPIcs.DNA.31.11},
  annote =	{Keywords: DNA strand displacement, strand-displacing polymerases, molecular computation, energy barriers, kinetics}
}
Document
Media Exposition
DOI: 10.4230/LIPIcs.SoCG.2025.81
AmoebotSim 2.0: A Visual Simulation Environment for the Amoebot Model with Reconfigurable Circuits and Joint Movements (Media Exposition)

Authors: Matthias Artmann, Tobias Maurer, Andreas Padalkin, Daniel Warner, and Christian Scheideler

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
We present AmoebotSim 2.0, a simulation environment for the geometric amoebot model of programmable matter that supports the reconfigurable circuit and joint movement extensions of the model. In the geometric amoebot model, we consider systems of simple computational entities called amoebots in a regular triangular grid environment. We are interested in distributed algorithms that solve coordination and shape formation problems. The reconfigurable circuit and joint movement extensions of the model allow the amoebots to communicate over greater distances and perform more complex movements, overcoming some limitations of the original model. AmoebotSim 2.0 is an open-source simulation environment that supports these extensions and provides a rich graphical interface, flexible simulation features, an extensive API, and comprehensive documentation.
Cite as

Matthias Artmann, Tobias Maurer, Andreas Padalkin, Daniel Warner, and Christian Scheideler. AmoebotSim 2.0: A Visual Simulation Environment for the Amoebot Model with Reconfigurable Circuits and Joint Movements (Media Exposition). In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 81:1-81:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{artmann_et_al:LIPIcs.SoCG.2025.81,
  author =	{Artmann, Matthias and Maurer, Tobias and Padalkin, Andreas and Warner, Daniel and Scheideler, Christian},
  title =	{{AmoebotSim 2.0: A Visual Simulation Environment for the Amoebot Model with Reconfigurable Circuits and Joint Movements}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{81:1--81:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.81},
  URN =		{urn:nbn:de:0030-drops-232338},
  doi =		{10.4230/LIPIcs.SoCG.2025.81},
  annote =	{Keywords: Programmable matter, amoebot model, reconfigurable circuits, joint movements, simulator}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.DNA.28
LIPIcs, Volume 238, DNA 28, Complete Volume

Authors: Thomas E. Ouldridge and Shelley F. J. Wickham

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
LIPIcs, Volume 238, DNA 28, Complete Volume
Cite as

28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 1-198, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Proceedings{ouldridge_et_al:LIPIcs.DNA.28,
  title =	{{LIPIcs, Volume 238, DNA 28, Complete Volume}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{1--198},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28},
  URN =		{urn:nbn:de:0030-drops-167843},
  doi =		{10.4230/LIPIcs.DNA.28},
  annote =	{Keywords: LIPIcs, Volume 238, DNA 28, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.DNA.28.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Thomas E. Ouldridge and Shelley F. J. Wickham

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{ouldridge_et_al:LIPIcs.DNA.28.0,
  author =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.0},
  URN =		{urn:nbn:de:0030-drops-167857},
  doi =		{10.4230/LIPIcs.DNA.28.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.1
Fast and Robust Strand Displacement Cascades via Systematic Design Strategies

Authors: Tiernan Kennedy, Cadence Pearce, and Chris Thachuk

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
A barrier to wider adoption of molecular computation is the difficulty of implementing arbitrary chemical reaction networks (CRNs) that are robust and replicate the kinetics of designed behavior. DNA Strand Displacement (DSD) cascades have been a favored technology for this purpose due to their potential to emulate arbitrary CRNs and known principles to tune their reaction rates. Progress on leakless cascades has demonstrated that DSDs can be arbitrarily robust to spurious "leak" reactions when incorporating systematic domain level redundancy. These improvements in robustness result in slower kinetics of designed reactions. Existing work has demonstrated the kinetic and thermodynamic effects of sequence mismatch introduction and elimination during displacement. We present a systematic, sequence modification strategy for optimizing the kinetics of leakless cascades without practical cost to their robustness. An in-depth case study explores the effects of this optimization when applied to a typical leakless translator cascade. Thermodynamic analysis of energy barriers and kinetic experimental data support that DSD cascades can be fast and robust.
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Tiernan Kennedy, Cadence Pearce, and Chris Thachuk. Fast and Robust Strand Displacement Cascades via Systematic Design Strategies. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 1:1-1:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{kennedy_et_al:LIPIcs.DNA.28.1,
  author =	{Kennedy, Tiernan and Pearce, Cadence and Thachuk, Chris},
  title =	{{Fast and Robust Strand Displacement Cascades via Systematic Design Strategies}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{1:1--1:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.1},
  URN =		{urn:nbn:de:0030-drops-167869},
  doi =		{10.4230/LIPIcs.DNA.28.1},
  annote =	{Keywords: DNA strand displacement, Energy barriers, Kinetics}
}
Document
Extended Abstract
DOI: 10.4230/LIPIcs.DNA.28.2
Universal Shape Replication via Self-Assembly with Signal-Passing Tiles (Extended Abstract)

Authors: Andrew Alseth, Daniel Hader, and Matthew J. Patitz

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
In this paper, we investigate shape-assembling power of a tile-based model of self-assembly called the Signal-Passing Tile Assembly Model (STAM). In this model, the glues that bind tiles together can be turned on and off by the binding actions of other glues via "signals". In fact, we prove our positive results in a version of the model in which it is slightly more difficult to work (where tiles are allowed to rotate) but show that they also hold in the standard STAM. Specifically, the problem we investigate is "shape replication" wherein, given a set of input assemblies of arbitrary shape, a system must construct an arbitrary number of assemblies with the same shapes and, with the exception of size-bounded junk assemblies that result from the process, no others. We provide the first fully universal shape replication result, namely a single tile set capable of performing shape replication on arbitrary sets of any 3-dimensional shapes without requiring any scaling or pre-encoded information in the input assemblies. Our result requires the input assemblies to be composed of signal-passing tiles whose glues can be deactivated to allow deconstruction of those assemblies, which we also prove is necessary by showing that there are shapes whose geometry cannot be replicated without deconstruction. Additionally, we modularize our construction to create systems capable of creating binary encodings of arbitrary shapes, and building arbitrary shapes from their encodings. Because the STAM is capable of universal computation, this then allows for arbitrary programs to be run within an STAM system, using the shape encodings as input, so that any computable transformation can be performed on the shapes.
Cite as

Andrew Alseth, Daniel Hader, and Matthew J. Patitz. Universal Shape Replication via Self-Assembly with Signal-Passing Tiles (Extended Abstract). In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 2:1-2:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{alseth_et_al:LIPIcs.DNA.28.2,
  author =	{Alseth, Andrew and Hader, Daniel and Patitz, Matthew J.},
  title =	{{Universal Shape Replication via Self-Assembly with Signal-Passing Tiles}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{2:1--2:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.2},
  URN =		{urn:nbn:de:0030-drops-167876},
  doi =		{10.4230/LIPIcs.DNA.28.2},
  annote =	{Keywords: Algorithmic self-assembly, Tile Assembly Model, shape replication}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.3
A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems

Authors: Hope Amber Johnson and Anne Condon

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
DNA Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound DNA strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms - sequences of basic reaction rules - that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with DNA. Here we introduce a new mechanism, which we call controlled reconfiguration. We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties; for example it is capable of implementing reversible CRNs and uses just two distinct toeholds. We discuss drawbacks of our implementation, particularly the reliance on pseudoknot-freeness for correctness, and suggest directions for future research that can provide further insight on the capabilities and limitations of controlled reconfiguration.
Cite as

Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{johnson_et_al:LIPIcs.DNA.28.3,
  author =	{Johnson, Hope Amber and Condon, Anne},
  title =	{{A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{3:1--3:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.3},
  URN =		{urn:nbn:de:0030-drops-167889},
  doi =		{10.4230/LIPIcs.DNA.28.3},
  annote =	{Keywords: Molecular programming, DNA Strand Displacement, Chemical Reaction Networks}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.4
Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm

Authors: Kuan-Lin Chen and Rebecca Schulman

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from advances in artificial intelligence and their applications in material discovery, we propose a computational method for designing metamorphic DNA-co-polymerized hydrogel structures. The method consists of a coarse-grained simulation and a deep learning-guided optimization system for exploring the immense design space of these structures. Here, we develop a simple numeric simulation of DNA-co-polymerized hydrogel shape change and seek to find designs for structured hydrogels that can fold into the shapes of different Arabic numerals in different actuation states. We train a convolutional neural network to classify and score the geometric outputs of the coarse-grained simulation to provide autonomous feedback for design optimization. We then construct a genetic algorithm that generates and selects large batches of material designs that compete with one another to evolve and converge on optimal objective-matching designs. We show that we are able to explore the large design space and learn important parameters and traits. We identify vital relationships between the material scale size and the range of shape change that can be achieved by individual domains and we elucidate trade-offs between different design parameters. Finally, we discover material designs capable of transforming into multiple different digits in different actuation states.
Cite as

Kuan-Lin Chen and Rebecca Schulman. Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{chen_et_al:LIPIcs.DNA.28.4,
  author =	{Chen, Kuan-Lin and Schulman, Rebecca},
  title =	{{Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{4:1--4:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.4},
  URN =		{urn:nbn:de:0030-drops-167899},
  doi =		{10.4230/LIPIcs.DNA.28.4},
  annote =	{Keywords: Machine Learning, Deep Learning, Computational Material Design, Multi-Objective Optimization, DNA Nanotechnology}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.5
Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking

Authors: Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield.
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Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani. Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{li_et_al:LIPIcs.DNA.28.5,
  author =	{Li, Bowen and Mackenzie, Neil and Shirt-Ediss, Ben and Krasnogor, Natalio and Zuliani, Paolo},
  title =	{{Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.5},
  URN =		{urn:nbn:de:0030-drops-167904},
  doi =		{10.4230/LIPIcs.DNA.28.5},
  annote =	{Keywords: probabilistic model checking, CTMC, DNA computing, DNA stack}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.6
On Turedo Hierarchies and Intrinsic Universality

Authors: Samuel Nalin and Guillaume Theyssier

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
This paper is about turedos, which are Turing machines whose head can move in the plane (or in a higher-dimensional space) but only in a self-avoiding way, by putting marks (letters) on visited positions and moving only to unmarked, therefore unvisited, positions. The turedo model has been introduced recently as a useful abstraction of oritatami systems, which where established a few years ago as a theoretical model of RNA co-transcriptional folding. The key parameter of turedos is their lookup radius: the distance up to which the head can look around in order to make its decision of where to move to and what mark to write. In this paper we study the hierarchy of turedos according to their lookup radius and the dimension of space using notions of simulation up to spatio-temporal rescaling (a standard approach in cellular automata or self-assembly systems). We establish that there is a rich interplay between the turedo parameters and the notion of simulation considered. We show in particular, for the most liberal simulations, the existence of 3D turedos of radius 1 that are intrinsically universal for all radii, but that this is impossible in dimension 2, where some radius 2 turedo are impossible to simulate at radius 1. Using stricter notions of simulation, intrinsic universality becomes impossible, even in dimension 3, and there is a strict radius hierarchy. Finally, when restricting to radius 1, universality is again possible in dimension 3, but not in dimension 2, where we show however that a radius 3 turedo can simulate all radius 1 turedos.
Cite as

Samuel Nalin and Guillaume Theyssier. On Turedo Hierarchies and Intrinsic Universality. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{nalin_et_al:LIPIcs.DNA.28.6,
  author =	{Nalin, Samuel and Theyssier, Guillaume},
  title =	{{On Turedo Hierarchies and Intrinsic Universality}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.6},
  URN =		{urn:nbn:de:0030-drops-167915},
  doi =		{10.4230/LIPIcs.DNA.28.6},
  annote =	{Keywords: Turedos, intrinsic universality, Higher-dimensional Turing machines, Oritatami systems}
}
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