13 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
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-dev.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-dev.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.
Cite as

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-dev.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-dev.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-dev.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-dev.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.
Cite as

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-dev.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-dev.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}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.7
Computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria

Authors: Xiang Huang and Rachel N. Huls

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

Abstract
Bournez, Fraigniaud, and Koegler [Bournez et al., 2012] defined a number in [0,1] as computable by their Large-Population Protocol (LPP) model, if the proportion of agents in a set of marked states converges to said number over time as the population grows to infinity. The notion, however, restricts the ordinary differential equations (ODEs) associated with an LPP to have only finitely many equilibria. This restriction places an intrinsic limitation on the model. As a result, a number is computable by an LPP if and only if it is algebraic, namely, not a single transcendental number can be computed under this notion. In this paper, we lift the finitary requirement on equilibria. That is, we consider systems with a continuum of equilibria. We show that essentially all numbers in [0,1] that are computable by bounded general-purpose analog computers (GPACs) or chemical reaction networks (CRNs) can also be computed by LPPs under this new definition. This implies a rich series of numbers (e.g., the reciprocal of Euler’s constant, π/4, Euler’s γ, Catalan’s constant, and Dottie number) are all computable by LPPs. Our proof is constructive: We develop an algorithm that transfers bounded GPACs/CRNs into LPPs. Our algorithm also fixes a gap in Bournez et al.’s construction of LPPs designed to compute any arbitrary algebraic number in [0,1].
Cite as

Xiang Huang and Rachel N. Huls. Computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 7:1-7:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{huang_et_al:LIPIcs.DNA.28.7,
  author =	{Huang, Xiang and Huls, Rachel N.},
  title =	{{Computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{7:1--7:22},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.7},
  URN =		{urn:nbn:de:0030-drops-167922},
  doi =		{10.4230/LIPIcs.DNA.28.7},
  annote =	{Keywords: Population protocols, Chemical reaction networks, Analog computation}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.8
The Structural Power of Reconfigurable Circuits in the Amoebot Model

Authors: Andreas Padalkin, Christian Scheideler, and Daniel Warner

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

Abstract
The amoebot model [Derakhshandeh et al., SPAA 2014] has been proposed as a model for programmable matter consisting of tiny, robotic elements called amoebots. We consider the reconfigurable circuit extension [Feldmann et al., JCB 2022] of the geometric (variant of the) amoebot model that allows the amoebot structure to interconnect amoebots by so-called circuits. A circuit permits the instantaneous transmission of signals between the connected amoebots. In this paper, we examine the structural power of the reconfigurable circuits. We start with some fundamental problems like the stripe computation problem where, given any connected amoebot structure S, an amoebot u in S, and some axis X, all amoebots belonging to axis X through u have to be identified. Second, we consider the global maximum problem, which identifies an amoebot at the highest possible position with respect to some direction in some given amoebot (sub)structure. A solution to this problem can then be used to solve the skeleton problem, where a (not necessarily simple) cycle of amoebots has to be found in the given amoebot structure which contains all boundary amoebots. A canonical solution to that problem can then be used to come up with a canonical path, which provides a unique characterization of the shape of the given amoebot structure. Constructing canonical paths for different directions will then allow the amoebots to set up a spanning tree and to check symmetry properties of the given amoebot structure. The problems are important for a number of applications like rapid shape transformation, energy dissemination, and structural monitoring. Interestingly, the reconfigurable circuit extension allows polylogarithmic-time solutions to all of these problems.
Cite as

Andreas Padalkin, Christian Scheideler, and Daniel Warner. The Structural Power of Reconfigurable Circuits in the Amoebot Model. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 8:1-8:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{padalkin_et_al:LIPIcs.DNA.28.8,
  author =	{Padalkin, Andreas and Scheideler, Christian and Warner, Daniel},
  title =	{{The Structural Power of Reconfigurable Circuits in the Amoebot Model}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{8:1--8:22},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.8},
  URN =		{urn:nbn:de:0030-drops-167935},
  doi =		{10.4230/LIPIcs.DNA.28.8},
  annote =	{Keywords: progammable matter, amoebot model, reconfigurable circuits, spanning tree, symmetry detection}
}
Document
DOI: 10.4230/LIPIcs.DNA.28.9
Fault-Tolerant Shape Formation in the Amoebot Model

Authors: Irina Kostitsyna, Christian Scheideler, and Daniel Warner

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

Abstract
The amoebot model is a distributed computing model of programmable matter. It envisions programmable matter as a collection of computational units called amoebots or particles that utilize local interactions to achieve tasks of coordination, movement and conformation. In the geometric amoebot model the particles operate on a hexagonal tessellation of the plane. Within this model, numerous problems such as leader election, shape formation or object coating have been studied. One area that has not received much attention so far, but is highly relevant for a practical implementation of programmable matter, is fault tolerance. The existing literature on that aspect allows particles to crash but assumes that crashed particles do not recover. We proposed a new model [Kostitsyna et al., 2022] in which a crash causes the memory of a particle to be reset and a crashed particle can detect that it has crashed and try to recover using its local information and communication capabilities. We present an algorithm that solves the hexagon shape formation problem in our model if a finite number of crashes occur and a designated leader particle does not fail. At the heart of our solution lies a fault-tolerant implementation of the spanning forest primitive, which, since other algorithms in the amoebot model also make use of it, is also of general interest.
Cite as

Irina Kostitsyna, Christian Scheideler, and Daniel Warner. Fault-Tolerant Shape Formation in the Amoebot Model. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 9:1-9:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

Copy BibTex To Clipboard

@InProceedings{kostitsyna_et_al:LIPIcs.DNA.28.9,
  author =	{Kostitsyna, Irina and Scheideler, Christian and Warner, Daniel},
  title =	{{Fault-Tolerant Shape Formation in the Amoebot Model}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{9:1--9:22},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.9},
  URN =		{urn:nbn:de:0030-drops-167949},
  doi =		{10.4230/LIPIcs.DNA.28.9},
  annote =	{Keywords: programmable matter, amoebot model, fault tolerance, shape formation}
}
Document
DOI: 10.4230/LIPIcs.DNA.2020.7
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

Authors: Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)

Abstract
DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct "catalyst" strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and the "identity" strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.
Cite as

Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge. Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 7:1-7:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

Copy BibTex To Clipboard

@InProceedings{lankinen_et_al:LIPIcs.DNA.2020.7,
  author =	{Lankinen, Antti and Mullor Ruiz, Ismael and Ouldridge, Thomas E.},
  title =	{{Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{7:1--7:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.7},
  URN =		{urn:nbn:de:0030-drops-129602},
  doi =		{10.4230/LIPIcs.DNA.2020.7},
  annote =	{Keywords: DNA strand displacement, Catalysis, Information-processing networks}
}
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