56 Search Results for "Doty, David"

Volume

LIPIcs, Volume 257

2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

SAND 2023, June 19-21, 2023, Pisa, Italy

Editors: David Doty and Paul Spirakis

Document
DOI: 10.4230/LIPIcs.DNA.32.1
Sequential Non-Determinism in Tile Self-Assembly: A General Framework and an Application to Efficient Temperature-1 Self-Assembly of Squares

Authors: David Furcy and Scott M. Summers

Published in: LIPIcs, Volume 387, 32nd International Conference on DNA Computing and Molecular Programming (DNA 32) (2026)

Abstract
In this paper, we work in a 2D version of the probabilistic variant of Winfree’s abstract Tile Assembly Model defined by Chandran, Gopalkrishnan and Reif (SICOMP 2012) in which attaching tiles are sampled uniformly with replacement. First, we develop a framework called "sequential non-determinism" for analyzing the probabilistic correctness of a non-deterministic, temperature-1 tile assembly system (TAS) in which most (but not all) tile attachments are deterministic and the non-deterministic attachments always occur in a specific order. Our main sequential non-determinism result equates the probabilistic correctness of such a TAS to a finite product of probabilities, each of which (1) corresponds to the probability of the correct type of tile attaching at a point where it is possible for two different types to attach, and (2) ignores all other tile attachments that do not affect the non-deterministic attachment. We then show that sequential non-determinism allows for efficient and geometrically expressive self-assembly. To that end, we constructively prove that for any positive integer N and any real δ ∈ (0,1), there exists a TAS that self-assembles into an N × N square with probability at least 1 - δ using only O(log N + log 1/(δ)) types of tiles. Our bound improves upon the previous state-of-the-art bound for this problem by Cook, Fu and Schweller (SODA 2011).
Cite as

David Furcy and Scott M. Summers. Sequential Non-Determinism in Tile Self-Assembly: A General Framework and an Application to Efficient Temperature-1 Self-Assembly of Squares. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 1:1-1:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{furcy_et_al:LIPIcs.DNA.32.1,
  author =	{Furcy, David and Summers, Scott M.},
  title =	{{Sequential Non-Determinism in Tile Self-Assembly: A General Framework and an Application to Efficient Temperature-1 Self-Assembly of Squares}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{1:1--1:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-444-4},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{387},
  editor =	{Scalise, Dominic and Schweller, Robert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.32.1},
  URN =		{urn:nbn:de:0030-drops-267710},
  doi =		{10.4230/LIPIcs.DNA.32.1},
  annote =	{Keywords: Self-assembly, tile assembly model, temperature 1, high probability self-assembly}
}
Document
DOI: 10.4230/LIPIcs.DNA.32.6
Reverse-Robust Computation with Chemical Reaction Networks

Authors: Ravi Kini and David Doty

Published in: LIPIcs, Volume 387, 32nd International Conference on DNA Computing and Molecular Programming (DNA 32) (2026)

Abstract
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all chemical reactions are reversible, even at very slow rates. We study the computational power of CRNs under the reverse-robust computation model, where reactions are permitted to occur either in forward or in reverse up to a cutoff point, after which they may only occur in forward. Our main results show that all semilinear predicates and all semilinear functions can be computed reverse-robustly, and in fact, that existing constructions continue to hold under the reverse-robust computational model. A key tool used to prove correctness under the reverse-robust computation model is invariants: linear (or linear modulo some m) combinations of the counts of the species that are preserved by all reactions.
Cite as

Ravi Kini and David Doty. Reverse-Robust Computation with Chemical Reaction Networks. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kini_et_al:LIPIcs.DNA.32.6,
  author =	{Kini, Ravi and Doty, David},
  title =	{{Reverse-Robust Computation with Chemical Reaction Networks}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{6:1--6:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-444-4},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{387},
  editor =	{Scalise, Dominic and Schweller, Robert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.32.6},
  URN =		{urn:nbn:de:0030-drops-267769},
  doi =		{10.4230/LIPIcs.DNA.32.6},
  annote =	{Keywords: chemical reaction networks, reverse-robust computation, semilinear}
}
Document
DOI: 10.4230/LIPIcs.DNA.32.11
Universal Spatial Distribution Approximation in Equilibrium Lattice Models with Local Pairwise Interactions

Authors: Cameron Chalk and Erik Winfree

Published in: LIPIcs, Volume 387, 32nd International Conference on DNA Computing and Molecular Programming (DNA 32) (2026)

Abstract
Universality is one of the defining hallmarks of a useful neural network model: it means that the model is expressive enough, in principle, to learn arbitrary target behavior rather than being limited to a narrow class. Inspired by rigorous formal analogies between stochastic neural networks and lattice models in which molecules occupy discrete sites, contribute species-dependent interaction energies with neighbors, and rearrange according to the Boltzmann distribution, we ask whether interactions can be programmed to yield arbitrary spatial distributions. At the level of fine-grained spatial arrangements of species, universality fails: arbitrary spatial microstate distributions cannot be represented, as shown by a counting argument and explicit construction of unrepresentable distributions. Yet, for a natural observable - spatial patterns of molecular labels - universality can be achieved. We show that a grand-canonical lattice model of anisotropic molecules is universal for arbitrary label distributions, and a similar model with isotropic molecules is also universal given a simple symmetry-breaking boundary condition. Our results suggest that equilibrium systems of multivalent molecules undergoing stochastic rearrangement governed by local pairwise interactions can act similarly to probabilistic neural networks: with sufficient microstate detail in hidden dimensions, they can be universal in a meaningful macrostate observable.
Cite as

Cameron Chalk and Erik Winfree. Universal Spatial Distribution Approximation in Equilibrium Lattice Models with Local Pairwise Interactions. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 11:1-11:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{chalk_et_al:LIPIcs.DNA.32.11,
  author =	{Chalk, Cameron and Winfree, Erik},
  title =	{{Universal Spatial Distribution Approximation in Equilibrium Lattice Models with Local Pairwise Interactions}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{11:1--11:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-444-4},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{387},
  editor =	{Scalise, Dominic and Schweller, Robert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.32.11},
  URN =		{urn:nbn:de:0030-drops-267812},
  doi =		{10.4230/LIPIcs.DNA.32.11},
  annote =	{Keywords: universality, molecular programming, neural networks, self-assembly}
}
Document
DOI: 10.4230/LIPIcs.SWAT.2026.3
Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks

Authors: Divya Bajaj, Bin Fu, Ryan Knobel, Austin Luchsinger, Aiden Massie, Pablo Santos, Ramiro Santos, Robert Schweller, Evan Tomai, and Tim Wylie

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
Chemical Reaction Networks (CRNs) are a well-established model of distributed computing characterized by quantities of molecular species that can transform or change through applications of reactions. A fundamental problem in CRNs is the reachability problem, which asks if an initial configuration of species can transition to a target configuration through an applicable sequence of reactions. It is well-known that the reachability problem in general CRNs was recently proven to be Ackermann-complete. However, if the CRN’s reactions are restricted in both power, such as only deleting species (deletion-only rules) or consuming and producing an equal number of species (volume-preserving rules), and size (unimolecular or bimolecular rules), then reachability falls below Ackermann-completeness, and is even solvable in polynomial time for deletion-only systems. In this paper, we investigate reachability under this set of restricted unimolecular and bimolecular reactions, but in the Priority-Inhibitory CRN and Inhibitory CRN models. These models extend a traditional CRN by allowing some reactions to be inhibited from firing in a configuration if certain species are present; the exact inhibition behavior varies between the models. We first show that reachability with Priority iCRNs mostly remains in P for deletion-only systems, but becomes NP-complete for one case. We then show that reachability with deletion-only reactions for iCRNs is mostly NP-complete, and PSPACE-complete even for (1,1)-size (general) reactions. We also provide FPT algorithms for solving most of the reachability problems for the iCRN model. Finally, we show reachability for CRNs with states is already NP-hard for the simplest deletion-only systems, and is PSPACE-complete even for (general) (1,1)-size reactions.
Cite as

Divya Bajaj, Bin Fu, Ryan Knobel, Austin Luchsinger, Aiden Massie, Pablo Santos, Ramiro Santos, Robert Schweller, Evan Tomai, and Tim Wylie. Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bajaj_et_al:LIPIcs.SWAT.2026.3,
  author =	{Bajaj, Divya and Fu, Bin and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Santos, Pablo and Santos, Ramiro and Schweller, Robert and Tomai, Evan and Wylie, Tim},
  title =	{{Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{3:1--3:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.3},
  URN =		{urn:nbn:de:0030-drops-260399},
  doi =		{10.4230/LIPIcs.SWAT.2026.3},
  annote =	{Keywords: Chemical Reaction Networks, Vector Addition Systems, Petri-nets, Reachability, Inhibitors, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.FUN.2026.29
Finding Shortest Walks in Kuru Kuru Kururin

Authors: Mickaël Laurent and Maher Mallem

Published in: LIPIcs, Volume 366, 13th International Conference on Fun with Algorithms (FUN 2026)

Abstract
This paper serves as a celebration of the twenty-fifth anniversary of Kuru Kuru Kururin. Although this video game is presented as a collection of two-dimensional puzzles based on rotation, it naturally invites players to complete its levels as quickly as possible. This has led to a surprisingly rich and challenging playing field to finding foremost temporal walks. In this work, we tackle this problem both in theory and in practice. First, we introduce a model for the game and provide an in-depth complexity analysis. Most notably, we show how each gameplay mechanic independently brings a layer of NP-hardness and/or co-NP-hardness. We also provide a pseudo-polynomial time algorithm for the general problem and identify several cases which can be solved in polynomial time. Along the way, we discuss connections to the more established framework of temporal graphs, both in the point model and the interval model. Then, we propose simple and flexible algorithmic techniques to reduce state space and guide the search, offering trade-offs between precision and computation speed in practice. These techniques were implemented and tested using a full recreation of the game physics and the levels from the original game. We demonstrate the efficiency of our framework in several settings - with or without taking damage, with or without unintended game mechanics - and relate empirical struggles which we encountered in practice to our complexity analysis. Our implementation is open source and fully available online, offering a novel and amusing setting to benchmark shortest path algorithms.
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Mickaël Laurent and Maher Mallem. Finding Shortest Walks in Kuru Kuru Kururin. In 13th International Conference on Fun with Algorithms (FUN 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 366, pp. 29:1-29:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{laurent_et_al:LIPIcs.FUN.2026.29,
  author =	{Laurent, Micka\"{e}l and Mallem, Maher},
  title =	{{Finding Shortest Walks in Kuru Kuru Kururin}},
  booktitle =	{13th International Conference on Fun with Algorithms (FUN 2026)},
  pages =	{29:1--29:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-417-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{366},
  editor =	{Iacono, John},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2026.29},
  URN =		{urn:nbn:de:0030-drops-257480},
  doi =		{10.4230/LIPIcs.FUN.2026.29},
  annote =	{Keywords: Shortest path, Complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.36
Beyond 2-Edge-Connectivity: Algorithms and Impossibility for Content-Oblivious Leader Election

Authors: Yi-Jun Chang, Lyuting Chen, and Haoran Zhou

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
The content-oblivious model, introduced by Censor-Hillel, Cohen, Gelles, and Sela (PODC 2022; Distributed Computing 2023), captures an extremely weak form of communication where nodes can only send asynchronous, content-less pulses. They showed that in 2-edge-connected networks, any distributed algorithm can be simulated in the content-oblivious model, provided that a unique leader is designated a priori. Subsequent works of Frei, Gelles, Ghazy, and Nolin (DISC 2024) and Chalopin et al. (DISC 2025) developed content-oblivious leader election algorithms, first for unoriented rings and then for general 2-edge-connected graphs. These results establish that all graph problems are solvable in content-oblivious, 2-edge-connected networks. Much less is known about networks that are not 2-edge-connected. Censor-Hillel, Cohen, Gelles, and Sela showed that no non-constant function f(x,y) can be computed correctly by two parties using content-oblivious communication over a single edge, where one party holds x and the other holds y. This seemingly ruled out many natural graph problems on non-2-edge-connected graphs. In this work, we show that, with the knowledge of network topology G, leader election is possible in a wide range of graphs. Our main contributions are as follows: Impossibility: Graphs symmetric about an edge admit no randomized terminating leader election algorithm, even when nodes have unique identifiers and full knowledge of G. Leader election algorithms: Trees that are not symmetric about any edge admit a quiescently terminating leader election algorithm with topology knowledge, even in anonymous networks, using O(n²) messages, where n is the number of nodes. Moreover, even-diameter trees admit a terminating leader election given only the knowledge of the network diameter D = 2r, with message complexity O(nr). Necessity of topology knowledge: In the family of graphs 𝒢 = {P₃, P₅}, both the 3-path P₃ and the 5-path P₅ admit a quiescently terminating leader election if nodes know the topology exactly. However, if nodes only know that the underlying topology belongs to 𝒢, then terminating leader election is impossible.
Cite as

Yi-Jun Chang, Lyuting Chen, and Haoran Zhou. Beyond 2-Edge-Connectivity: Algorithms and Impossibility for Content-Oblivious Leader Election. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 36:1-36:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{chang_et_al:LIPIcs.ITCS.2026.36,
  author =	{Chang, Yi-Jun and Chen, Lyuting and Zhou, Haoran},
  title =	{{Beyond 2-Edge-Connectivity: Algorithms and Impossibility for Content-Oblivious Leader Election}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{36:1--36:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.36},
  URN =		{urn:nbn:de:0030-drops-253239},
  doi =		{10.4230/LIPIcs.ITCS.2026.36},
  annote =	{Keywords: Asynchronous model, fault tolerance, quiescent termination}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2025.30
Byzantine-Tolerant Phase Clock

Authors: Costas Busch, Paweł Garncarek, and Dariusz R. Kowalski

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)

Abstract
A phase clock is a basic synchronization mechanism that keeps distributed nodes closely synchronized to execute the same phase of a distributed algorithm. A phase clock is typically implemented with a local logical counter that keeps track of the current phase count. Phase clocks are particularly useful in population protocols for implementing leader election and majority selection. We study phase clocks that tolerate Byzantine faults. We show that there is a phase clock that tolerates up to f < n/3 faulty nodes, where n is the number of nodes, such that the gap of the local counter values is O(n²log n). The gap can be further lowered to O(log n) when f ≤ n/8. We also show that if f > n/3, then the gap grows to infinity as time increases. While analyzing phase clock we introduce novel techniques and bounds for balls into bins processes, which might be of independent interest. Using the phase clock, we obtain a majority selection population protocol that tolerates up to f faults and decides on the majority value in O(log² n) parallel time using poly-log states per node.
Cite as

Costas Busch, Paweł Garncarek, and Dariusz R. Kowalski. Byzantine-Tolerant Phase Clock. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 30:1-30:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{busch_et_al:LIPIcs.OPODIS.2025.30,
  author =	{Busch, Costas and Garncarek, Pawe{\l} and Kowalski, Dariusz R.},
  title =	{{Byzantine-Tolerant Phase Clock}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{30:1--30:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.30},
  URN =		{urn:nbn:de:0030-drops-252036},
  doi =		{10.4230/LIPIcs.OPODIS.2025.30},
  annote =	{Keywords: phase clock, Byzantine nodes, population protocols, balls into bins}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.7
Polynomial Equivalence of Extended Chemical Reaction Models

Authors: Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
The ability to detect whether a species (or dimension) is zero in Chemical Reaction Networks (CRN), Vector Addition Systems, or Petri Nets is known to increase the power of these models - making them capable of universal computation. While this ability may appear in many forms, such as extending the models to allow transitions to be inhibited, prioritized, or synchronized, we present an extension that directly performs this zero checking. We introduce a new void genesis CRN variant with a simple design that merely increments the count of a specific species when any other species' count goes to zero. As with previous extensions, we show that the model is Turing Universal. We then analyze several other studied CRN variants and show that they are all equivalent through a polynomial simulation with the void genesis model, which does not merely follow from Turing-universality. Thus, inhibitor species, reactions that occur at different rates, being allowed to run reactions in parallel, or even being allowed to continually add more volume to the CRN, does not add additional simulation power beyond simply detecting if a species count becomes zero.
Cite as

Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie. Polynomial Equivalence of Extended Chemical Reaction Models. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 7:1-7:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bajaj_et_al:LIPIcs.ISAAC.2025.7,
  author =	{Bajaj, Divya and Castellanos, Jose-Luis and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Salinas, Adrian and Santos, Pablo and Santos, Ramiro and Schweller, Robert and Wylie, Tim},
  title =	{{Polynomial Equivalence of Extended Chemical Reaction Models}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{7:1--7:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.7},
  URN =		{urn:nbn:de:0030-drops-249158},
  doi =		{10.4230/LIPIcs.ISAAC.2025.7},
  annote =	{Keywords: Chemical Reaction Networks, Simulations, Petri-nets, Vector Addition Systems, Bi-simulation, Turing-universality, Inhibitors}
}
Document
DOI: 10.4230/LIPIcs.DISC.2025.21
Content-Oblivious Leader Election in 2-Edge-Connected Networks

Authors: Jérémie Chalopin, Yi-Jun Chang, Lyuting Chen, Giuseppe A. Di Luna, and Haoran Zhou

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

Abstract
Censor-Hillel, Cohen, Gelles, and Sela (PODC 2022 & Distributed Computing 2023) studied fully-defective asynchronous networks, where communication channels may arbitrarily corrupt messages. The model is equivalent to content-oblivious computation, where nodes communicate solely via pulses. They showed that if the network is 2-edge-connected, then any algorithm for a noiseless setting can be simulated in the fully-defective setting; otherwise, no non-trivial computation is possible in the fully-defective setting. However, their simulation requires a predesignated leader, which they conjectured to be necessary for any non-trivial content-oblivious task. Recently, Frei, Gelles, Ghazy, and Nolin (DISC 2024) refuted this conjecture for the special case of oriented ring topology. They designed two asynchronous content-oblivious leader election algorithms with message complexity O(n ⋅ ID_{max}), where n is the number of nodes and ID_{max} is the maximum ID. The first algorithm stabilizes in unoriented rings without termination detection. The second algorithm quiescently terminates in oriented rings, thus enabling the execution of the simulation algorithm after leader election. In this work, we present two results: General 2-edge-connected topologies: First, we show an asynchronous content-oblivious leader election algorithm that quiescently terminates in any 2-edge-connected network with message complexity O(m ⋅ N ⋅ ID_{min}), where m is the number of edges, N is a known upper bound on the number of nodes, and ID_{min} is the smallest ID. Combined with the above simulation, this result shows that whenever a size bound N is known, any noiseless algorithm can be simulated in the fully-defective model without a preselected leader, fully refuting the conjecture. Unoriented rings: We then show that the knowledge of N can be dropped in unoriented ring topologies by presenting a quiescently terminating election algorithm with message complexity O(n ⋅ ID_{max}) that matches the previous bound. Consequently, this result constitutes a strict improvement over the previous state of the art and shows that, on rings, fully-defective and noiseless communication are computationally equivalent, with no additional assumptions.
Cite as

Jérémie Chalopin, Yi-Jun Chang, Lyuting Chen, Giuseppe A. Di Luna, and Haoran Zhou. Content-Oblivious Leader Election in 2-Edge-Connected Networks. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 21:1-21:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chalopin_et_al:LIPIcs.DISC.2025.21,
  author =	{Chalopin, J\'{e}r\'{e}mie and Chang, Yi-Jun and Chen, Lyuting and Di Luna, Giuseppe A. and Zhou, Haoran},
  title =	{{Content-Oblivious Leader Election in 2-Edge-Connected Networks}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{21:1--21:22},
  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.2025.21},
  URN =		{urn:nbn:de:0030-drops-248385},
  doi =		{10.4230/LIPIcs.DISC.2025.21},
  annote =	{Keywords: Asynchronous model, fault tolerance, quiescent termination}
}
Document
DOI: 10.4230/LIPIcs.DISC.2025.19
Robust Predicate and Function Computation in Continuous Chemical Reaction Networks

Authors: Kim Calabrese, David Doty, and Mina Latifi

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

Abstract
We initiate the study of "rate-constant-independent" computation of Boolean predicates (decision problems) and numerical functions in the continuous model of chemical reaction networks (CRNs), which model the amount of a chemical species as a nonnegative, real-valued concentration, representing an average count per unit volume. Real-valued numerical functions have previously been studied [Chen et al., 2023], finding that exactly the continuous, piecewise rational linear (meaning linear with rational slopes) functions f: ℝ_{>0}^k → ℝ_{>0} can be computed stably (a.k.a., rate-independently), meaning roughly that the CRN gets the answer correct no matter the rate at which reactions occur. For example the reactions X₁ → Y and X₂+Y → ∅, starting with inputs X₁ ≥ X₂, converge to output Y having concentration equal to the initial difference of inputs X₁ - X₂, no matter the relative rate at which each reaction proceeds. We first show that, contrary to the case of real-valued functions, continuous CRNs are severely limited in the Boolean predicates they can stably decide, reporting a yes/no answer based only on which inputs are 0 or positive, but not on the exact positive value of any input. This limitation motivates a slightly relaxed notion of rate-independent computation in CRNs that we call robust computation. The standard mass-action rate model is used, in which each reaction (e.g., A+B →^k C) is assigned a rate (A ⋅ B ⋅ k in this example) equal to the product of its reactant concentrations and its rate constant k. We say the computation is correct in this model if it converges to the correct output for any positive choice of rate constants. This adversary is weaker than the adversary defining stable computation, the latter being able to run reactions at rates that are not those of mass-action for any choice of rate constants (e.g., the stable adversary may deactivate a reaction temporarily, even if all reactants are positive). We show that CRNs can robustly decide every predicate that is a finite Boolean combination of threshold predicates, where a threshold predicate is defined by taking a rational weighted sum of the inputs x ∈ ℝ^k_{≥ 0} and comparing to a constant, answering the question "Is ∑_{i = 1}^k w_i ⋅ x(i) > h?", for rational weights w_i and real threshold h. Turning to function computation, we show that CRNs can robustly compute any piecewise affine function with rational coefficients, where threshold predicates determine which affine piece to evaluate for a given input x.
Cite as

Kim Calabrese, David Doty, and Mina Latifi. Robust Predicate and Function Computation in Continuous Chemical Reaction Networks. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{calabrese_et_al:LIPIcs.DISC.2025.19,
  author =	{Calabrese, Kim and Doty, David and Latifi, Mina},
  title =	{{Robust Predicate and Function Computation in Continuous Chemical Reaction Networks}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{19:1--19:23},
  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.2025.19},
  URN =		{urn:nbn:de:0030-drops-248368},
  doi =		{10.4230/LIPIcs.DISC.2025.19},
  annote =	{Keywords: chemical reaction networks, analog computation, mean-field limit}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.20
Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR

Authors: Bryson Lawton, Frank Maurer, and Daniel Zielasko

Published in: OASIcs, Volume 130, Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)

Abstract
With thousands of exoplanets now confirmed by space missions such as NASA’s Kepler and TESS, scientific interest and public curiosity about these distant worlds continue to grow. However, current visualization tools for exploring exoplanetary systems often lack sufficient scientific accuracy or interactive features, limiting their educational effectiveness and analytical utility. To help address this gap, we developed ExoAR, an augmented reality tool designed to offer immersive, scientifically sound visualizations of all known exoplanetary systems using data directly sourced from NASA’s Exoplanet Archive. By leveraging augmented reality’s strengths, ExoAR enables users to immerse themselves in interactive, dynamic 3D models of these planetary systems with data-driven representations of planets and their host stars. The application also allows users to adjust various visualization scales independently, a capability designed to aid comprehension of comparative astronomical properties such as orbital mechanics, planetary sizes, and stellar classifications. To begin assessing ExoAR’s potential as an educational and analytical tool and inform future iterations, a pilot user study was conducted. Its findings indicate that participants found ExoAR improved user engagement and spatial understanding compared to NASA’s Eyes on Exoplanets application, a non-immersive exoplanetary system visualization tool. This work-in-progress paper presents these early insights, acknowledges current system limitations, and outlines future directions for more rigorously evaluating and further improving ExoAR’s capabilities for both educational and scientific communities.
Cite as

Bryson Lawton, Frank Maurer, and Daniel Zielasko. Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 20:1-20:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lawton_et_al:OASIcs.SpaceCHI.2025.20,
  author =	{Lawton, Bryson and Maurer, Frank and Zielasko, Daniel},
  title =	{{Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{20:1--20:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.20},
  URN =		{urn:nbn:de:0030-drops-240106},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.20},
  annote =	{Keywords: Immersive Analytics, Data Visualization, Astronomy, Astrophysics, Exoplanet, Augmented Reality, AR}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.1
Algorithmic Hardness of the Partition Function for Nucleic Acid Strands

Authors: Gwendal Ducloz, Ahmed Shalaby, and Damien Woods

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

Abstract
To understand and engineer biological and artificial nucleic acid systems, algorithms are employed for prediction of secondary structures at thermodynamic equilibrium. Dynamic programming algorithms are used to compute the most favoured, or Minimum Free Energy (MFE), structure, and the Partition Function (PF) - a tool for assigning a probability to any structure. However, in some situations, such as when there are large numbers of strands, or pseudoknotted systems, NP-hardness results show that such algorithms are unlikely, but only for MFE. Curiously, algorithmic hardness results were not shown for PF, leaving two open questions on the complexity of PF for multiple strands and single strands with pseudoknots. The challenge is that while the MFE problem cares only about one, or a few structures, PF is a summation over the entire secondary structure space, giving theorists the vibe that computing PF should not only be as hard as MFE, but should be even harder. We answer both questions. First, we show that computing PF is #P-hard for systems with an unbounded number of strands, answering a question of Condon Hajiaghayi, and Thachuk [DNA27]. Second, for even a single strand, but allowing pseudoknots, we find that PF is #P-hard. Our proof relies on a novel magnification trick that leads to a tightly-woven set of reductions between five key thermodynamic problems: MFE, PF, their decision versions, and #SSEL that counts structures of a given energy. Our reductions show these five problems are fundamentally related for any energy model amenable to magnification. That general classification clarifies the mathematical landscape of nucleic acid energy models and yields several open questions.
Cite as

Gwendal Ducloz, Ahmed Shalaby, and Damien Woods. Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ducloz_et_al:LIPIcs.DNA.31.1,
  author =	{Ducloz, Gwendal and Shalaby, Ahmed and Woods, Damien},
  title =	{{Algorithmic Hardness of the Partition Function for Nucleic Acid Strands}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{1:1--1:23},
  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.31.1},
  URN =		{urn:nbn:de:0030-drops-238504},
  doi =		{10.4230/LIPIcs.DNA.31.1},
  annote =	{Keywords: Partition function, minimum free energy, nucleic acid, DNA, RNA, secondary structure, computational complexity, #P-hardness}
}
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.31.7
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}
}
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