30 Search Results for "Soloveichik, David"

Document
DOI: 10.4230/LIPIcs.DNA.32.8
Amplification at Equilibrium: Structural and Thermodynamic Limitations, and Implementation

Authors: Hamidreza Akef, Chia-Yu Sung, Aneesh Vanguri, and David Soloveichik

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

Abstract
Amplifying weak molecular signals is essential in both natural and engineered biochemical systems. While most amplification schemes operate out of equilibrium, relying on kinetic barriers and fuel-driven cascades, it is also possible to amplify at thermodynamic equilibrium by shifting the energy landscape upon addition of an analyte. Equilibrium amplification is appealing because, in principle, the system can remain indefinitely in the untriggered state. In this work, we establish fundamental structural and thermodynamic limits on equilibrium-based amplification. We first prove that dimerization networks - systems restricted to complexes of at most two monomers - are inherently incapable of equilibrium amplification. This no-go theorem explains the absence of amplification in prior undercomplementary "strand commutation" designs. We then show that allowing trimeric complexes breaks this barrier. We propose an isometric trimer-based equilibrium amplifier whose output preserves the size of the input, enabling modular composition, and validate it experimentally, achieving an amplification factor close to the expected 2×. Finally, we derive universal thermodynamic bounds applicable regardless of complex size: the maximum amplification factor scales linearly with the free energy of interaction between the analyte and the amplifier components. For nucleic acid systems, this implies that the analyte length must grow linearly with the desired amplification factor, and that composing modular amplifiers yields diminishing returns for a fixed analyte. Together, these results delineate the structural and energetic boundaries of equilibrium amplification and rigorously justify the necessity of out-of-equilibrium approaches for achieving high gain.
Cite as

Hamidreza Akef, Chia-Yu Sung, Aneesh Vanguri, and David Soloveichik. Amplification at Equilibrium: Structural and Thermodynamic Limitations, and Implementation. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 8:1-8:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{akef_et_al:LIPIcs.DNA.32.8,
  author =	{Akef, Hamidreza and Sung, Chia-Yu and Vanguri, Aneesh and Soloveichik, David},
  title =	{{Amplification at Equilibrium: Structural and Thermodynamic Limitations, and Implementation}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{8:1--8:24},
  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.32.8},
  URN =		{urn:nbn:de:0030-drops-267789},
  doi =		{10.4230/LIPIcs.DNA.32.8},
  annote =	{Keywords: Equilibrium amplification, Dimerization networks, Strand commutation, Thermodynamics of amplification}
}
Document
DOI: 10.4230/LIPIcs.DNA.32.9
Thermodynamic Binding Networks Capture Equilibrium Monomer-Polymer Thermodynamics

Authors: And Kaan Ata Yilmaz, David Soloveichik, and Austin Luchsinger

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

Abstract
Thermodynamic Binding Networks (TBNs) are a minimal model for molecular thermodynamics. Despite their simplicity, the stable behavior of these systems can be unexpectedly nontrivial. To better understand the expressive power of the model, we compare TBNs with Thermodynamic Affinity Networks (TANs), a partition-scoring formalism in which polymer-level favorability is specified directly, rather than derived from domain-level interactions. We show that these two models are thermodynamically equivalent at the level of stable configurations: every TBN can be represented directly by a TAN, and every TAN can be indirectly realized by a TBN whose stable configurations map exactly to the stable configurations of the TAN. The key idea in the latter direction is to use auxiliary monomers that allow the system to convert polymer-level free-energy rewards specified by the TAN into entropic gains from separate complexes in the TBN. This correspondence shows that the local rules of TBNs do not limit their equilibrium expressive power nearly as much as one might expect. In this minimum-free-energy sense of equilibrium, TBNs capture the coarse-grained monomer-polymer thermodynamics formalized by TANs.
Cite as

And Kaan Ata Yilmaz, David Soloveichik, and Austin Luchsinger. Thermodynamic Binding Networks Capture Equilibrium Monomer-Polymer Thermodynamics. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{yilmaz_et_al:LIPIcs.DNA.32.9,
  author =	{Yilmaz, And Kaan Ata and Soloveichik, David and Luchsinger, Austin},
  title =	{{Thermodynamic Binding Networks Capture Equilibrium Monomer-Polymer Thermodynamics}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{9:1--9:20},
  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.32.9},
  URN =		{urn:nbn:de:0030-drops-267796},
  doi =		{10.4230/LIPIcs.DNA.32.9},
  annote =	{Keywords: Thermodynamic Binding Networks, Thermodynamic Affinity Networks, Equilibrium Thermodynamics}
}
Document
DOI: 10.4230/LIPIcs.DNA.32.10
Modularity of Signal Propagation Networks in the Thermodynamic Binding Network Model

Authors: And Kaan Ata Yilmaz and David Soloveichik

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

Abstract
The Thermodynamic Binding Network (TBN) model provides an equilibrium-based abstraction for molecular systems, but proving correctness of large networks built from individually verified modules remains difficult because modules can interact through shared binding-site types. We develop a method for proving correctness of modular TBNs by reducing a composition of arbitrarily many modules to a fixed coarse-grained TBN, computing the Hilbert basis of the reduced system, and lifting the resulting entropy bounds and polymer characterizations back to the original network. We apply this method to reversible signal-propagation modules: For the previously studied module implementing A+B ⟷ C, we show that stable configurations of an arbitrary network of such modules have the intended local structure, implying that firing an individual module preserves global stability. Under certain restrictions on the reaction set, these networks faithfully simulate a class of reversible chemical reaction networks: every bounded-length CRN execution can be realized by a height-2 path between stable TBN configurations, and any two stable TBN configurations map to CRN states in the same stoichiometric compatibility class. We further show that the same proof strategy extends to a novel module implementing reactions with two reactants and products like A+B ⟷ C+D.
Cite as

And Kaan Ata Yilmaz and David Soloveichik. Modularity of Signal Propagation Networks in the Thermodynamic Binding Network Model. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 10:1-10:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{yilmaz_et_al:LIPIcs.DNA.32.10,
  author =	{Yilmaz, And Kaan Ata and Soloveichik, David},
  title =	{{Modularity of Signal Propagation Networks in the Thermodynamic Binding Network Model}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{10:1--10:23},
  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.32.10},
  URN =		{urn:nbn:de:0030-drops-267809},
  doi =		{10.4230/LIPIcs.DNA.32.10},
  annote =	{Keywords: Thermodynamic Binding Networks, Chemical Reaction Networks, Modular Composition, Verification, Simulation}
}
Document
DOI: 10.4230/LIPIcs.DNA.32.12
Scalable Enumeration of Pareto-Optimal Polymers for Computing Equilibrium Concentrations

Authors: Archit Patil, Minki Hhan, and David Soloveichik

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

Abstract
Predicting equilibrium concentrations of molecular complexes is essential for verifying the behavior of engineered DNA systems. However, a finite set of monomer types can in principle generate infinitely many complexes. We study this candidate-enumeration problem in a geometry-free, domain-level abstraction called a domain-monomer system, generalizing Thermodynamic Binding Networks (TBNs) to the unsaturated setting where not every possible bond need be formed. We define Pareto-suboptimal polymers as those that can be split into non-interacting parts, and show that restricting attention to Pareto-optimal polymers is thermodynamically justified: no Pareto-suboptimal polymer appears in any minimum free-energy configuration, and the total equilibrium concentration of such polymers is small. We prove that there are finitely many Pareto-optimal polymers and exactly characterize them via a Hilbert basis computation, extending prior work from the saturated TBN model. To scale this approach to large systems, we develop a framework that restricts the number of different monomer types that a single polymer contains, and uses combinatorial covering designs to reduce the number of Hilbert basis computations required. We benchmark the method on several families of DNA molecular programming systems, demonstrating order-of-magnitude speedups over direct computation while recovering nearly all equilibrium-relevant polymers.
Cite as

Archit Patil, Minki Hhan, and David Soloveichik. Scalable Enumeration of Pareto-Optimal Polymers for Computing Equilibrium Concentrations. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 12:1-12:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{patil_et_al:LIPIcs.DNA.32.12,
  author =	{Patil, Archit and Hhan, Minki and Soloveichik, David},
  title =	{{Scalable Enumeration of Pareto-Optimal Polymers for Computing Equilibrium Concentrations}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{12:1--12:24},
  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.32.12},
  URN =		{urn:nbn:de:0030-drops-267823},
  doi =		{10.4230/LIPIcs.DNA.32.12},
  annote =	{Keywords: Molecular computation, Hilbert Basis, Thermodynamic Binding Network, covering design, equilibrium concentration}
}
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)

Copy BibTex To Clipboard

@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.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)

Copy BibTex To Clipboard

@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.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)

Copy BibTex To Clipboard

@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)

Copy BibTex To Clipboard

@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.MFCS.2025.11
Universality Frontier for Asynchronous Cellular Automata

Authors: Ivan Baburin, Matthew Cook, Florian Grötschla, Andreas Plesner, and Roger Wattenhofer

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
In this work, we investigate computational aspects of asynchronous cellular automata (ACAs), a modification of cellular automata in which cells update independently, following an asynchronous update schedule. We introduce flip automata networks (FANs), a simple modification of automata networks that remain robust under any asynchronous updating order. By using FANs as a middleman, we show that asynchronous automata can efficiently simulate their synchronous counterparts with a linear memory overhead, which improves upon the previously established quadratic bound. Additionally, we address the universality gap for (a)synchronous cellular automata-the boundary separating universal and non-universal automata, which is still not fully understood. We tighten this boundary by proving that all one-way asynchronous automata lack universal computational power. Conversely, we establish the existence of a universal asynchronous 6-state first-neighbor automaton in one dimension and a 3-state von Neumann automaton in two dimensions, which represent the smallest known universal constructions to date.
Cite as

Ivan Baburin, Matthew Cook, Florian Grötschla, Andreas Plesner, and Roger Wattenhofer. Universality Frontier for Asynchronous Cellular Automata. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 11:1-11:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{baburin_et_al:LIPIcs.MFCS.2025.11,
  author =	{Baburin, Ivan and Cook, Matthew and Gr\"{o}tschla, Florian and Plesner, Andreas and Wattenhofer, Roger},
  title =	{{Universality Frontier for Asynchronous Cellular Automata}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{11:1--11:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.11},
  URN =		{urn:nbn:de:0030-drops-241182},
  doi =		{10.4230/LIPIcs.MFCS.2025.11},
  annote =	{Keywords: Universality, Asynchronous Cellular Automata, Automata Networks}
}
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)

Copy BibTex To Clipboard

@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.31.3
Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

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

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Our results provide a nearly complete classification of void-rule reachability problems into tractable and intractable cases, with only a single exception.
Cite as

Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{fu_et_al:LIPIcs.DNA.31.3,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{3:1--3:21},
  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.31.3},
  URN =		{urn:nbn:de:0030-drops-238521},
  doi =		{10.4230/LIPIcs.DNA.31.3},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
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)

Copy BibTex To Clipboard

@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.31.8
An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming

Authors: Matthew J. Patitz and Trent A. Rogers

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

Abstract
In this paper we present a theoretical design for tile-based self-assembling systems where individual tile sets that are universal for various tasks (e.g. building shapes or encoding arbitrary data for algorithmic systems) can be provided their input solely using sequences of variations in temperatures. Although there is prior theoretical work in so-called "temperature programming," the results presented here are based upon recent experimental work with "blocked tiles" that provides plausible evidence for their practical implementation. We develop and present an abstract mathematical model, the BlockTAM, for such systems that is based upon the experimental work, and provide constructions within it for universal number encoding systems and a universal shape building construction. These results mirror previous results in temperature programming, covering the two ends of the spectrum that seek to balance the scale factors of assemblies with the number of temperature phases required, while leveraging the features of the BlockTAM that we hope provide a pathway for future experimental implementations.
Cite as

Matthew J. Patitz and Trent A. Rogers. An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{patitz_et_al:LIPIcs.DNA.31.8,
  author =	{Patitz, Matthew J. and Rogers, Trent A.},
  title =	{{An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{8:1--8:20},
  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.31.8},
  URN =		{urn:nbn:de:0030-drops-238574},
  doi =		{10.4230/LIPIcs.DNA.31.8},
  annote =	{Keywords: DNA tiles, self-assembly, temperature programming}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.10
Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems

Authors: Hamidreza Akef, Minki Hhan, and David Soloveichik

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

Abstract
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form complexes (polymers). Rather than employing free-energy parameters for each polymer, we focus on the athermic setting where all interactions preserve enthalpy. This setting aligns with the strongly bonded (domain-based) regime in DNA nanotechnology when strands can bind in different ways, but always with maximum overall bonding - and is consistent with the saturated configurations in the Thermodynamic Binding Networks (TBNs) model. Within this context, we develop an iterative algorithm for assigning polymer concentrations to satisfy detailed-balance, where on-target (desired) polymers are in high concentrations and off-target (undesired) polymers are in low. Even if not directly executed, our algorithm provides effective insights into upper bounds on concentration of off-target polymers, connecting combinatorial arguments about discrete configurations such as those in the TBN model to real-valued concentrations. We conclude with an application of our method to decreasing leak in DNA logic and signal propagation. Our results offer a new framework for design and verification of equilibrium concentrations when configurations are distinguished by entropic forces.
Cite as

Hamidreza Akef, Minki Hhan, and David Soloveichik. Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 10:1-10:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{akef_et_al:LIPIcs.DNA.31.10,
  author =	{Akef, Hamidreza and Hhan, Minki and Soloveichik, David},
  title =	{{Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{10:1--10:19},
  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.31.10},
  URN =		{urn:nbn:de:0030-drops-238595},
  doi =		{10.4230/LIPIcs.DNA.31.10},
  annote =	{Keywords: Equilibrium concentrations, Thermodynamic Binding Networks, Monomer-polymer model, Detailed balance}
}
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)

Copy BibTex To Clipboard

@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}
}
  • Refine by Type
  • 30 Document/PDF
  • 16 Document/HTML

  • Refine by Publication Year
  • 6 2026
  • 14 2025
  • 4 2023
  • 1 2022
  • 2 2021
  • Show More...

  • Refine by Author
  • 10 Soloveichik, David
  • 7 Luchsinger, Austin
  • 5 Doty, David
  • 5 Knobel, Ryan
  • 5 Schweller, Robert
  • Show More...

  • Refine by Series/Journal
  • 30 LIPIcs

  • Refine by Classification
  • 14 Theory of computation → Models of computation
  • 4 Computer systems organization → Molecular computing
  • 3 Theory of computation
  • 2 Applied computing → Chemistry
  • 2 Applied computing → Computational biology
  • Show More...

  • Refine by Keyword
  • 5 Chemical Reaction Networks
  • 3 DNA strand displacement
  • 3 Reachability
  • 3 Thermodynamic Binding Networks
  • 3 Void Reactions
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact