47 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.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}
}
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)

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@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.31.9
Synchronous Versus Asynchronous Tile-Based Self-Assembly

Authors: Florent Becker, Phillip Drake, 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 study the relationship between mathematical models of tile-based self-assembly which differ in terms of the synchronicity of tile additions. In the standard abstract Tile Assembly Model (aTAM), each step of assembly consists of a single tile being added to an assembly. At any given time, each location on the perimeter of an assembly to which a tile can legally bind is called a frontier location, and for each step of assembly one frontier location is randomly selected and a tile is added. In the Synchronous Tile Assembly Model (syncTAM), at each step of assembly every frontier location simultaneously receives a tile. Our results show that while directed, non-cooperative syncTAM systems are capable of universal computation (while directed, non-cooperative aTAM systems are known not to be), and they are capable of building shapes that can't be built within the aTAM, the non-cooperative aTAM is also capable of building shapes that can't be built within the syncTAM even cooperatively. We show a variety of results that demonstrate the similarities and differences between these two models.
Cite as

Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers. Synchronous Versus Asynchronous Tile-Based Self-Assembly. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{becker_et_al:LIPIcs.DNA.31.9,
  author =	{Becker, Florent and Drake, Phillip and Patitz, Matthew J. and Rogers, Trent A.},
  title =	{{Synchronous Versus Asynchronous Tile-Based Self-Assembly}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{9:1--9:21},
  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.31.9},
  URN =		{urn:nbn:de:0030-drops-238580},
  doi =		{10.4230/LIPIcs.DNA.31.9},
  annote =	{Keywords: self-assembly, noncooperative self-assembly, models of computation, tile assembly systems}
}
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)

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@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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.130
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands

Authors: Ahmed Shalaby and Damien Woods

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
The information-encoding molecules RNA and DNA bind via base pairing to form an exponentially large set of secondary structures. Practitioners need algorithms to predict the most favoured structures, called minimum free energy (MFE) structures, or to compute a partition function that allows assigning a probability to any structure. MFE prediction is NP-hard in the presence pseudoknots - base pairings that violate a restricted planarity condition. However, for single-stranded unpseudoknotted structures, there are polynomial time dynamic programming algorithms. For multiple strands, the problem is significantly more complicated: Codon, Hajiaghayi and Thachuk [DNA27, 2021] proved it NP-hard for N bases and 𝒪(N) strands. Dirks, Bois, Schaeffer, Winfree and Pierce [SIAM Review, 2007] gave a polynomial time partition function algorithm for multiple (𝒪(1)) strands, now widely-used, however their technique did not generalise to MFE which they left open. We give an 𝒪(N⁴) time algorithm for unpseudoknotted multiple (𝒪(1)) strand MFE prediction, answering the open problem from Dirks et al. The challenge lies in considering the rotational symmetry of secondary structures, a global feature not immediately amenable to local subproblem decomposition used in dynamic programming. Our proof has two main technical contributions: First, a characterisation of symmetric secondary structures implying only quadratically many need to be considered when computing the rotational symmetry penalty. Second, that bound is leveraged by a backtracking algorithm to efficiently find the MFE in an exponential space of contenders.
Cite as

Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130,
  author =	{Shalaby, Ahmed and Woods, Damien},
  title =	{{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{130:1--130:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.130},
  URN =		{urn:nbn:de:0030-drops-235071},
  doi =		{10.4230/LIPIcs.ICALP.2025.130},
  annote =	{Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.FORC.2025.17
Debiasing Functions of Private Statistics in Postprocessing

Authors: Flavio Calmon, Elbert Du, Cynthia Dwork, Brian Finley, and Grigory Franguridi

Published in: LIPIcs, Volume 329, 6th Symposium on Foundations of Responsible Computing (FORC 2025)

Abstract
Given a differentially private unbiased estimate q̃ = q(D) +ν of a statistic q(D), we wish to obtain unbiased estimates of functions of q(D), such as 1/q(D), solely through post-processing of q̃, with no further access to the confidential dataset D. To this end, we adapt the deconvolution method used for unbiased estimation in the statistical literature, deriving unbiased estimators for a broad family of twice-differentiable functions - those that are tempered distributions - when the privacy-preserving noise ν is drawn from the Laplace distribution (Dwork et al., 2006). We further extend this technique to functions other than tempered distributions, deriving approximately optimal estimators that are unbiased for values in a user-specified interval (possibly extending to ± ∞). We use these results to derive an unbiased estimator for private means when the size n of the dataset is not publicly known. In a numerical application, we find that a mechanism that uses our estimator to return an unbiased sample size and mean outperforms a mechanism that instead uses the previously known unbiased privacy mechanism for such means (Kamath et al., 2023). We also apply our estimators to develop unbiased transformation mechanisms for per-record differential privacy, a privacy concept in which the privacy guarantee is a public function of a record’s value (Seeman et al., 2024). Our mechanisms provide stronger privacy guarantees than those in prior work (Finley et al., 2024) by using Laplace, rather than Gaussian, noise. Finally, using a different approach, we go beyond Laplace noise by deriving unbiased estimators for polynomials under the weak condition that the noise distribution has sufficiently many moments.
Cite as

Flavio Calmon, Elbert Du, Cynthia Dwork, Brian Finley, and Grigory Franguridi. Debiasing Functions of Private Statistics in Postprocessing. In 6th Symposium on Foundations of Responsible Computing (FORC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 329, pp. 17:1-17:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{calmon_et_al:LIPIcs.FORC.2025.17,
  author =	{Calmon, Flavio and Du, Elbert and Dwork, Cynthia and Finley, Brian and Franguridi, Grigory},
  title =	{{Debiasing Functions of Private Statistics in Postprocessing}},
  booktitle =	{6th Symposium on Foundations of Responsible Computing (FORC 2025)},
  pages =	{17:1--17:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-367-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{329},
  editor =	{Bun, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2025.17},
  URN =		{urn:nbn:de:0030-drops-231449},
  doi =		{10.4230/LIPIcs.FORC.2025.17},
  annote =	{Keywords: Differential privacy, deconvolution, unbiasedness}
}
Document
DOI: 10.4230/LIPIcs.SAND.2025.1
The Expressive Power of Uniform Population Protocols with Logarithmic Space

Authors: Philipp Czerner, Vincent Fischer, and Roland Guttenberg

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
Population protocols are a model of computation in which indistinguishable mobile agents interact in pairs to decide a property of their initial configuration. Originally introduced by Angluin et. al. in 2004 with a constant number of states, research nowadays focuses on protocols where the space usage depends on the number of agents. The expressive power of population protocols has so far however only been determined for protocols using o(log n) states, which compute only semilinear predicates, and for Ω(n) states. This leaves a significant gap, particularly concerning protocols with Θ(log n) or Θ(polylog n) states, which are the most common constructions in the literature. In this paper we close the gap and prove that for any ε > 0 and f ∈ Ω(log n)∩𝒪(n^{1-ε}), both uniform and non-uniform population protocols with Θ(f(n)) states can decide exactly those predicates, whose unary encoding lies in NSPACE(f(n) log n).
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Philipp Czerner, Vincent Fischer, and Roland Guttenberg. The Expressive Power of Uniform Population Protocols with Logarithmic Space. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 1:1-1:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{czerner_et_al:LIPIcs.SAND.2025.1,
  author =	{Czerner, Philipp and Fischer, Vincent and Guttenberg, Roland},
  title =	{{The Expressive Power of Uniform Population Protocols with Logarithmic Space}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{1:1--1:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.1},
  URN =		{urn:nbn:de:0030-drops-230540},
  doi =		{10.4230/LIPIcs.SAND.2025.1},
  annote =	{Keywords: Population Protocols, Uniform, Expressive Power}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.SAND.2025.24
Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly

Authors: Tim Gomez, Elise Grizzell, Asher Haun, Ryan Knobel, Tom Peters, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
The Tile Automata (TA) model describes self-assembly systems in which monomers can build structures and transition with an adjacent monomer to change their states. This paper shows that seeded TA is a non-committal intrinsically universal model of self-assembly. We present a single universal Tile Automata system containing approximately 4600 states that can simulate (a) the output assemblies created by any other Tile Automata system Γ, (b) the dynamics involved in building Γ’s assemblies, and (c) Γ’s internal state transitions. It does so in a non-committal way: it preserves the full non-deterministic dynamics of a tile’s potential attachment or transition by selecting its state in a single step, considering all possible outcomes until the moment of selection. The system uses supertiles, each encoding the complete system being simulated. The universal system builds supertiles from its seed, each representing a single tile in Γ, transferring the information to simulate Γ to each new tile. Supertiles may also asynchronously transition states according to the rules of Γ. This result also implies IU for pairwise asynchronous Cellular Automata.
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Tim Gomez, Elise Grizzell, Asher Haun, Ryan Knobel, Tom Peters, Robert Schweller, and Tim Wylie. Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 24:1-24:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gomez_et_al:LIPIcs.SAND.2025.24,
  author =	{Gomez, Tim and Grizzell, Elise and Haun, Asher and Knobel, Ryan and Peters, Tom and Schweller, Robert and Wylie, Tim},
  title =	{{Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{24:1--24:6},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.24},
  URN =		{urn:nbn:de:0030-drops-230772},
  doi =		{10.4230/LIPIcs.SAND.2025.24},
  annote =	{Keywords: Intrinsic Universality, Tile Automata, Cellular Automata, Self-assembly}
}
Document
DOI: 10.4230/LIPIcs.SAND.2025.14
Fractals in Seeded Tile Automata

Authors: Asher Haun, Ryan Knobel, Adrian Salinas, Ramiro Santos, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
This work fully characterizes fractal generation in the seeded Tile Automata model (seeded TA), a model similar to the abstract Tile Assembly model (aTAM) with the added ability for adjacent tiles to change states. Under these assumptions, we first show that all discrete self-similar fractals (DSSFs) with feasible generators are strictly buildable at scale 1 and temperature 1 in seeded TA. We then show that these results imply the existence of a single seeded TA system Γ that can strictly build any DSSF infinitely at scale 1 and temperature 1.
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Asher Haun, Ryan Knobel, Adrian Salinas, Ramiro Santos, Robert Schweller, and Tim Wylie. Fractals in Seeded Tile Automata. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 14:1-14:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{haun_et_al:LIPIcs.SAND.2025.14,
  author =	{Haun, Asher and Knobel, Ryan and Salinas, Adrian and Santos, Ramiro and Schweller, Robert and Wylie, Tim},
  title =	{{Fractals in Seeded Tile Automata}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{14:1--14:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.14},
  URN =		{urn:nbn:de:0030-drops-230677},
  doi =		{10.4230/LIPIcs.SAND.2025.14},
  annote =	{Keywords: self-assembly, tile automata, fractals}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.37
Almost Time-Optimal Loosely-Stabilizing Leader Election on Arbitrary Graphs Without Identifiers in Population Protocols

Authors: Haruki Kanaya, Ryota Eguchi, Taisho Sasada, and Michiko Inoue

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
The population protocol model is a computational model for passive mobile agents. We address the leader election problem, which determines a unique leader on arbitrary communication graphs starting from any configuration. Unfortunately, self-stabilizing leader election is impossible to be solved without knowing the exact number of agents; thus, we consider loosely-stabilizing leader election, which converges to safe configurations in a relatively short time, and holds the specification (maintains a unique leader) for a relatively long time. When agents have unique identifiers, Sudo {et al. }(2019) proposed a protocol that, given an upper bound N for the number of agents n, converges in O(mNlog n) expected steps, where m is the number of edges. When unique identifiers are not required, they also proposed a protocol that, using random numbers and given N, converges in O(mN²log{N}) expected steps. Both protocols have a holding time of Ω(e^{2N}) expected steps and use O(log{N}) bits of memory. They also showed that the lower bound of the convergence time is Ω(mN) expected steps for protocols with a holding time of Ω(e^N) expected steps given N. In this paper, we propose protocols that do not require unique identifiers. These protocols achieve convergence times close to the lower bound with increasing memory usage. Specifically, given N and an upper bound Δ for the maximum degree, we propose two protocols whose convergence times are O(mNlog n) and O(mNlog N) both in expectation and with high probability. The former protocol uses random numbers, while the latter does not require them. Both protocols utilize O(Δ log N) bits of memory and hold the specification for Ω(e^{2N}) expected steps.
Cite as

Haruki Kanaya, Ryota Eguchi, Taisho Sasada, and Michiko Inoue. Almost Time-Optimal Loosely-Stabilizing Leader Election on Arbitrary Graphs Without Identifiers in Population Protocols. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 37:1-37:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kanaya_et_al:LIPIcs.OPODIS.2024.37,
  author =	{Kanaya, Haruki and Eguchi, Ryota and Sasada, Taisho and Inoue, Michiko},
  title =	{{Almost Time-Optimal Loosely-Stabilizing Leader Election on Arbitrary Graphs Without Identifiers in Population Protocols}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{37:1--37:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.37},
  URN =		{urn:nbn:de:0030-drops-225734},
  doi =		{10.4230/LIPIcs.OPODIS.2024.37},
  annote =	{Keywords: Population protocols, Leader election, Loose-stabilization, Self-stabilization}
}
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