33 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.2024.20
The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions

Authors: David Doty and Ben Heckmann

Published in: LIPIcs, Volume 319, 38th International Symposium on Distributed Computing (DISC 2024)

Abstract
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as A + B → C, representing that if a molecule of A and B collide, they disappear and a molecule of C is produced. CRNs can compute Boolean-valued predicates ϕ:ℕ^d → {0,1} and integer-valued functions f:ℕ^d → ℕ; for instance X₁ + X₂ → Y computes the function min(x₁,x₂), since starting with x_i copies of X_i, eventually min(x₁,x₂) copies of Y are produced. We study the computational power of execution bounded CRNs, in which only a finite number of reactions can occur from the initial configuration (e.g., ruling out reversible reactions such as A ⇌ B). The power and composability of such CRNs depend crucially on some other modeling choices that do not affect the computational power of CRNs with unbounded executions, namely whether an initial leader is present, and whether (for predicates) all species are required to "vote" for the Boolean output. If the CRN starts with an initial leader, and can allow only the leader to vote, then all semilinear predicates and functions can be stably computed in O(n log n) parallel time by execution bounded CRNs. However, if no initial leader is allowed, all species vote, and the CRN is "non-collapsing" (does not shrink from initially large to final O(1) size configurations), then execution bounded CRNs are severely limited, able to compute only eventually constant predicates. A key tool is a characterization of execution bounded CRNs as precisely those with a nonnegative linear potential function that is strictly decreased by every reaction [Czerner et al., 2024].
Cite as

David Doty and Ben Heckmann. The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions. In 38th International Symposium on Distributed Computing (DISC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 319, pp. 20:1-20:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{doty_et_al:LIPIcs.DISC.2024.20,
  author =	{Doty, David and Heckmann, Ben},
  title =	{{The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions}},
  booktitle =	{38th International Symposium on Distributed Computing (DISC 2024)},
  pages =	{20:1--20:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-352-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{319},
  editor =	{Alistarh, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2024.20},
  URN =		{urn:nbn:de:0030-drops-212469},
  doi =		{10.4230/LIPIcs.DISC.2024.20},
  annote =	{Keywords: chemical reaction networks, population protocols, stable computation}
}
Document
DOI: 10.4230/LIPIcs.DNA.29.1
Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer

Authors: Ahmed Shalaby, Chris Thachuk, and Damien Woods

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
Polynomial time dynamic programming algorithms play a crucial role in the design, analysis and engineering of nucleic acid systems including DNA computers and DNA/RNA nanostructures. However, in complex multistranded or pseudoknotted systems, computing the minimum free energy (MFE), and partition function of nucleic acid systems is NP-hard. Despite this, multistranded and/or pseudoknotted systems represent some of the most utilised and successful systems in the field. This leaves open the tempting possibility that many of the kinds of multistranded and/or pseudoknotted systems we wish to engineer actually fall into restricted classes, that do in fact have polynomial time algorithms, but we've just not found them yet. Here, we give polynomial time algorithms for MFE and partition function calculation for a restricted kind of multistranded system called the 1D scaffolded DNA computer. This model of computation thermodynamically favours correct outputs over erroneous states, simulates finite state machines in 1D and Boolean circuits in 2D, and is amenable to DNA storage applications. In an effort to begin to ask the question of whether we can naturally compare the expressivity of nucleic acid systems based on the computational complexity of prediction of their preferred energetic states, we show our MFE problem is in logspace (the complexity class L), making it perhaps one of the simplest known, natural, nucleic acid MFE problems. Finally, we provide a stochastic kinetic simulator for the 1D scaffolded DNA computer and evaluate strategies for efficiently speeding up this thermodynamically favourable system in a constant-temperature kinetic regime.
Cite as

Ahmed Shalaby, Chris Thachuk, and Damien Woods. Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 1:1-1:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{shalaby_et_al:LIPIcs.DNA.29.1,
  author =	{Shalaby, Ahmed and Thachuk, Chris and Woods, Damien},
  title =	{{Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{1:1--1:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.1},
  URN =		{urn:nbn:de:0030-drops-187840},
  doi =		{10.4230/LIPIcs.DNA.29.1},
  annote =	{Keywords: thermodynamic computation, model of computation, molecular computing, minimum free energy, partition function, DNA computing, DNA self-assembly, DNA strand displacement, kinetics simulation}
}
Document
DOI: 10.4230/LIPIcs.DNA.29.7
Accelerating Self-Assembly of Crisscross Slat Systems

Authors: David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
We present an abstract model of self-assembly of systems composed of "crisscross slats", which have been experimentally implemented as a single-stranded piece of DNA [Minev et al., 2021] or as a complete DNA origami structure [Wintersinger et al., 2022]. We then introduce a more physically realistic "kinetic" model and show how important constants in the model were derived and tuned, and compare simulation-based results to experimental results [Minev et al., 2021; Wintersinger et al., 2022]. Using these models, we show how we can apply optimizations to designs of slat systems in order to lower the numbers of unique slat types required to build target structures. In general, we apply two types of techniques to achieve greatly reduced numbers of slat types. Similar to the experimental work implementing DNA origami-based slats, in our designs the slats oriented in horizontal and vertical directions are each restricted to their own plane and sets of them overlap each other in square regions which we refer to as macrotiles. Our first technique extends their previous work of reusing slat types within macrotiles and requires analyses of binding domain patterns to determine the potential for errors consisting of incorrect slat types attaching at undesired translations and reflections. The second technique leverages the power of algorithmic self-assembly to efficiently reuse entire macrotiles which self-assemble in patterns following designed algorithms that dictate the dimensions and patterns of growth. Using these designs, we demonstrate that in kinetic simulations the systems with reduced numbers of slat types self-assemble more quickly than those with greater numbers. This provides evidence that such optimizations will also result in greater assembly speeds in experimental systems. Furthermore, the reduced numbers of slat types required have the potential to vastly reduce the cost and number of lab steps for crisscross assembly experiments.
Cite as

David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan. Accelerating Self-Assembly of Crisscross Slat Systems. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{doty_et_al:LIPIcs.DNA.29.7,
  author =	{Doty, David and Fleming, Hunter and Hader, Daniel and Patitz, Matthew J. and Vaughan, Lukas A.},
  title =	{{Accelerating Self-Assembly of Crisscross Slat Systems}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.7},
  URN =		{urn:nbn:de:0030-drops-187908},
  doi =		{10.4230/LIPIcs.DNA.29.7},
  annote =	{Keywords: DNA origami, self-assembly, kinetic modeling, computational modeling}
}
Document
DOI: 10.4230/LIPIcs.DNA.29.8
Thermodynamically Driven Signal Amplification

Authors: Joshua Petrack, David Soloveichik, and David Doty

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. By modeling this physical phenomenon at different levels of specificity, different operative computational behavior is observed. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which molecules are bound to each other in a "thermodynamically stable" sense. Stability is measured based only on how many bonds are formed and how many total complexes are in a configuration, without focusing on how molecules are binding or how they became bound. By defocusing on kinetic processes, TBNs attempt to naturally model the long-term behavior of a mixture (i.e., its thermodynamic equilibrium). We study the problem of signal amplification: detecting a small quantity of some molecule and amplifying its signal to something more easily detectable. This problem has natural applications such as disease diagnosis. By focusing on thermodynamically favored outcomes, we seek to design chemical systems that perform the task of signal amplification robustly without relying on kinetic pathways that can be error prone and require highly controlled conditions (e.g., PCR amplification). It might appear that a small change in concentrations can result in only small changes to the thermodynamic equilibrium of a molecular system. However, we show that it is possible to design a TBN that can "exponentially amplify" a signal represented by a single copy of a monomer called the analyte: this TBN has exactly one stable state before adding the analyte and exactly one stable state afterward, and those two states "look very different" from each other. In particular, their difference is exponential in the number of types of molecules and their sizes. The system can be programmed to any desired level of resilience to false positives and false negatives. To prove these results, we introduce new concepts to the TBN model, particularly the notions of a TBN’s entropy gap to describe how unlikely it is to be observed in an undesirable state, and feed-forward TBNs that have a strong upper bound on the number of polymers in a stable configuration. We also show a corresponding negative result: a doubly exponential upper bound, meaning that there is no TBN that can amplify a signal by an amount more than doubly exponential in the number and sizes of different molecules that comprise it. We leave as an open question to close this gap by either proving an exponential upper bound, or giving a construction with a doubly-exponential difference between the stable configurations before and after the analyte is added. Our work informs the fundamental question of how a thermodynamic equilibrium can change as a result of a small change to the system (adding a single molecule copy). While exponential amplification is traditionally viewed as inherently a non-equilibrium phenomenon, we find that in a strong sense exponential amplification can occur at thermodynamic equilibrium as well - where the "effect" (e.g., fluorescence) is exponential in types and complexity of the chemical components.
Cite as

Joshua Petrack, David Soloveichik, and David Doty. Thermodynamically Driven Signal Amplification. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 8:1-8:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{petrack_et_al:LIPIcs.DNA.29.8,
  author =	{Petrack, Joshua and Soloveichik, David and Doty, David},
  title =	{{Thermodynamically Driven Signal Amplification}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{8:1--8:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.8},
  URN =		{urn:nbn:de:0030-drops-187917},
  doi =		{10.4230/LIPIcs.DNA.29.8},
  annote =	{Keywords: Thermodynamic binding networks, signal amplification, integer programming}
}
Document
DOI: 10.4230/LIPIcs.DNA.29.9
Optimal Information Encoding in Chemical Reaction Networks

Authors: Austin Luchsinger, David Doty, and David Soloveichik

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has been widely studied in the molecular programming and distributed computing communities. While for Turing-universal systems there is a universal measure of optimal information encoding based on Kolmogorov complexity, chemical reaction networks are not Turing universal unless error and unbounded molecular counts are permitted. Nonetheless, here we show that the optimal number of reactions to generate a specific count x ∈ ℕ with probability 1 is asymptotically equal to a "space-aware" version of the Kolmogorov complexity of x, defined as K̃s(x) = min_p {|p|/log|p| + log(space(𝒰(p))) : 𝒰(p) = x}, where p is a program for universal Turing machine 𝒰. This version of Kolmogorov complexity incorporates not just the length of the shortest program for generating x, but also the space usage of that program. Probability 1 computation is captured by the standard notion of stable computation from distributed computing, but we limit our consideration to chemical reaction networks obeying a stronger constraint: they "know when they are done" in the sense that they produce a special species to indicate completion. As part of our results, we develop a module for encoding and unpacking any b bits of information via O(b/log{b}) reactions, which is information-theoretically optimal for incompressible information. Our work provides one answer to the question of how succinctly chemical self-organization can be encoded - in the sense of generating precise molecular counts of species as the desired state.
Cite as

Austin Luchsinger, David Doty, and David Soloveichik. Optimal Information Encoding in Chemical Reaction Networks. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{luchsinger_et_al:LIPIcs.DNA.29.9,
  author =	{Luchsinger, Austin and Doty, David and Soloveichik, David},
  title =	{{Optimal Information Encoding in Chemical Reaction Networks}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{9:1--9:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.9},
  URN =		{urn:nbn:de:0030-drops-187920},
  doi =		{10.4230/LIPIcs.DNA.29.9},
  annote =	{Keywords: chemical reaction networks, Kolmogorov complexity, stable computation}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2023.65
A Weyl Criterion for Finite-State Dimension and Applications

Authors: Jack H. Lutz, Satyadev Nandakumar, and Subin Pulari

Published in: LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)

Abstract
Finite-state dimension, introduced early in this century as a finite-state version of classical Hausdorff dimension, is a quantitative measure of the lower asymptotic density of information in an infinite sequence over a finite alphabet, as perceived by finite automata. Finite-state dimension is a robust concept that now has equivalent formulations in terms of finite-state gambling, lossless finite-state data compression, finite-state prediction, entropy rates, and automatic Kolmogorov complexity. The 1972 Schnorr-Stimm dichotomy theorem gave the first automata-theoretic characterization of normal sequences, which had been studied in analytic number theory since Borel defined them in 1909. This theorem implies, in present-day terminology, that a sequence (or a real number having this sequence as its base-b expansion) is normal if and only if it has finite-state dimension 1. One of the most powerful classical tools for investigating normal numbers is the 1916 Weyl’s criterion, which characterizes normality in terms of exponential sums. Such sums are well studied objects with many connections to other aspects of analytic number theory, and this has made use of Weyl’s criterion especially fruitful. This raises the question whether Weyl’s criterion can be generalized from finite-state dimension 1 to arbitrary finite-state dimensions, thereby making it a quantitative tool for studying data compression, prediction, etc. i.e., Can we characterize all compression ratios using exponential sums?. This paper does exactly this. We extend Weyl’s criterion from a characterization of sequences with finite-state dimension 1 to a criterion that characterizes every finite-state dimension. This turns out not to be a routine generalization of the original Weyl criterion. Even though exponential sums may diverge for non-normal numbers, finite-state dimension can be characterized in terms of the dimensions of the subsequence limits of the exponential sums. In case the exponential sums are convergent, they converge to the Fourier coefficients of a probability measure whose dimension is precisely the finite-state dimension of the sequence. This new and surprising connection helps us bring Fourier analytic techniques to bear in proofs in finite-state dimension, yielding a new perspective. We demonstrate the utility of our criterion by substantially improving known results about preservation of finite-state dimension under arithmetic. We strictly generalize the results by Aistleitner and Doty, Lutz and Nandakumar for finite-state dimensions under arithmetic operations. We use the method of exponential sums and our Weyl criterion to obtain the following new result: If y is a number having finite-state strong dimension 0, then dim_FS(x+qy) = dim_FS(x) and Dim_FS(x+qy) = Dim_FS(x) for any x ∈ ℝ and q ∈ ℚ. This generalization uses recent estimates obtained in the work of Hochman [Hochman, 2014] regarding the entropy of convolutions of probability measures.
Cite as

Jack H. Lutz, Satyadev Nandakumar, and Subin Pulari. A Weyl Criterion for Finite-State Dimension and Applications. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 65:1-65:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{lutz_et_al:LIPIcs.MFCS.2023.65,
  author =	{Lutz, Jack H. and Nandakumar, Satyadev and Pulari, Subin},
  title =	{{A Weyl Criterion for Finite-State Dimension and Applications}},
  booktitle =	{48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)},
  pages =	{65:1--65:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-292-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{272},
  editor =	{Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.65},
  URN =		{urn:nbn:de:0030-drops-185997},
  doi =		{10.4230/LIPIcs.MFCS.2023.65},
  annote =	{Keywords: Finite-state dimension, Finite-state compression, Weyl’s criterion, Exponential sums, Normal numbers}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.SAND.2023
LIPIcs, Volume 257, SAND 2023, Complete Volume

Authors: David Doty and Paul Spirakis

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
LIPIcs, Volume 257, SAND 2023, Complete Volume
Cite as

2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 1-278, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Proceedings{doty_et_al:LIPIcs.SAND.2023,
  title =	{{LIPIcs, Volume 257, SAND 2023, Complete Volume}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{1--278},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023},
  URN =		{urn:nbn:de:0030-drops-179357},
  doi =		{10.4230/LIPIcs.SAND.2023},
  annote =	{Keywords: LIPIcs, Volume 257, SAND 2023, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SAND.2023.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: David Doty and Paul Spirakis

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

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

2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{doty_et_al:LIPIcs.SAND.2023.0,
  author =	{Doty, David and Spirakis, Paul},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{0:i--0:x},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.0},
  URN =		{urn:nbn:de:0030-drops-179367},
  doi =		{10.4230/LIPIcs.SAND.2023.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.1
Snapshot Disjointness in Temporal Graphs

Authors: Allen Ibiapina and Ana Silva

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
In the study of temporal graphs, only paths respecting the flow of time are relevant. In this context, many concepts of walks disjointness have been proposed over the years, and the validity of Menger’s Theorem, as well as the complexity of related problems, has been investigated. Menger’s Theorem states that the maximum number of disjoint paths between two vertices is equal to the minimum number of vertices required to disconnect them. In this paper, we introduce and investigate a type of disjointness that is only time dependent. Two walks are said to be snapshot disjoint if they are not active in a same snapshot (also called timestep). The related paths and cut problems are then defined and proved to be W[1]-hard and XP-time solvable when parameterized by the size of the solution. Additionally, in the light of the definition of Mengerian graphs given by Kempe, Kleinberg and Kumar in their seminal paper (STOC'2000), we define a Mengerian graph for time as a graph G for which there is no time labeling for its edges where Menger’s Theorem does not hold in the context of snapshot disjointness. We then give a characterization of Mengerian graphs in terms of forbidden structures and provide a polynomial-time recognition algorithm. Finally, we also prove that, given a temporal graph (G,λ) and a pair of vertices s,z ∈ V(G), deciding whether at most h multiedges can separate s from z is NP-complete, where one multiedge uv is the set of all edges with endpoints u and v.
Cite as

Allen Ibiapina and Ana Silva. Snapshot Disjointness in Temporal Graphs. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{ibiapina_et_al:LIPIcs.SAND.2023.1,
  author =	{Ibiapina, Allen and Silva, Ana},
  title =	{{Snapshot Disjointness in Temporal Graphs}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.1},
  URN =		{urn:nbn:de:0030-drops-179379},
  doi =		{10.4230/LIPIcs.SAND.2023.1},
  annote =	{Keywords: Temporal graphs, Menger’s Theorem, Snapshot disjointness}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.2
Partial Gathering of Mobile Agents in Dynamic Tori

Authors: Masahiro Shibata, Naoki Kitamura, Ryota Eguchi, Yuichi Sudo, Junya Nakamura, and Yonghwan Kim

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
In this paper, we consider the partial gathering problem of mobile agents in synchronous dynamic tori. The partial gathering problem is a generalization of the (well-investigated) total gathering problem, which requires that all k agents distributed in the network terminate at a non-predetermined single node. The partial gathering problem requires, for a given positive integer g (< k), that agents terminate in a configuration such that either at least g agents or no agent exists at each node. So far, in almost cases, the partial gathering problem has been considered in static graphs. As only one exception, it is considered in a kind of dynamic rings called 1-interval connected rings, that is, one of the links in the ring may be missing at each time step. In this paper, we consider partial gathering in another dynamic topology. Concretely, we consider it in n× n dynamic tori such that each of row rings and column rings is represented as a 1-interval connected ring. In such networks, when k = O(gn), focusing on the relationship between the values of k, n, and g, we aim to characterize the solvability of the partial gathering problem and analyze the move complexity of the proposed algorithms when the problem can be solved. First, we show that agents cannot solve the problem when k = o(gn), which means that Ω (gn) agents are necessary to solve the problem. Second, we show that the problem can be solved with the total number of O(gn³) moves when 2gn+2n-1 ≤ k ≤ 2gn + 6n +16g -12. Finally, we show that the problem can be solved with the total number of O(gn²) moves when k ≥ 2gn + 6n +16g -11. From these results, we show that our algorithms can solve the partial gathering problem in dynamic tori with the asymptotically optimal number Θ (gn) of agents. In addition, we show that agents require a total number of Ω(gn²) moves to solve the partial gathering problem in dynamic tori when k = Θ(gn). Thus, when k ≥ 2gn+6n+16g -11, our algorithm can solve the problem with asymptotically optimal number O(gn²) of agent moves.
Cite as

Masahiro Shibata, Naoki Kitamura, Ryota Eguchi, Yuichi Sudo, Junya Nakamura, and Yonghwan Kim. Partial Gathering of Mobile Agents in Dynamic Tori. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 2:1-2:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{shibata_et_al:LIPIcs.SAND.2023.2,
  author =	{Shibata, Masahiro and Kitamura, Naoki and Eguchi, Ryota and Sudo, Yuichi and Nakamura, Junya and Kim, Yonghwan},
  title =	{{Partial Gathering of Mobile Agents in Dynamic Tori}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{2:1--2:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.2},
  URN =		{urn:nbn:de:0030-drops-179387},
  doi =		{10.4230/LIPIcs.SAND.2023.2},
  annote =	{Keywords: distributed system, mobile agents, partial gathering, dynamic tori}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.3
Bond Percolation in Small-World Graphs with Power-Law Distribution

Authors: Luca Becchetti, Andrea Clementi, Francesco Pasquale, Luca Trevisan, and Isabella Ziccardi

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
Full-bond percolation with parameter p is the process in which, given a graph, for every edge independently, we keep the edge with probability p and delete it with probability 1-p. Bond percolation is studied in parallel computing and network science to understand the resilience of distributed systems to random link failure and the spread of information in networks through unreliable links. Moreover, the full-bond percolation is equivalent to the Reed-Frost process, a network version of SIR epidemic spreading. We consider one-dimensional power-law small-world graphs with parameter α obtained as the union of a cycle with additional long-range random edges: each pair of nodes {u,v} at distance L on the cycle is connected by a long-range edge {u,v}, with probability proportional to 1/L^α. Our analysis determines three phases for the percolation subgraph G_p of the small-world graph, depending on the value of α. - If α < 1, there is a p < 1 such that, with high probability, there are Ω(n) nodes that are reachable in G_p from one another in 𝒪(log n) hops; - If 1 < α < 2, there is a p < 1 such that, with high probability, there are Ω(n) nodes that are reachable in G_p from one another in log^{𝒪(1)}(n) hops; - If α > 2, for every p < 1, with high probability all connected components of G_p have size 𝒪(log n).
Cite as

Luca Becchetti, Andrea Clementi, Francesco Pasquale, Luca Trevisan, and Isabella Ziccardi. Bond Percolation in Small-World Graphs with Power-Law Distribution. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 3:1-3:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{becchetti_et_al:LIPIcs.SAND.2023.3,
  author =	{Becchetti, Luca and Clementi, Andrea and Pasquale, Francesco and Trevisan, Luca and Ziccardi, Isabella},
  title =	{{Bond Percolation in Small-World Graphs with Power-Law Distribution}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{3:1--3:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.3},
  URN =		{urn:nbn:de:0030-drops-179392},
  doi =		{10.4230/LIPIcs.SAND.2023.3},
  annote =	{Keywords: Information spreading, gossiping, epidemics, fault-tolerance, network self-organization and formation, complex systems, social and transportation networks}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.4
Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time

Authors: Filippo Brunelli and Laurent Viennot

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
This paper proposes a simple algorithm for computing single-source reachability in a temporal graph under waiting-time constraints, that is when waiting at each node is bounded by some time constraints. Given a space-time representation of a temporal graph, and a source node, the algorithm computes in linear-time which nodes and temporal edges are reachable through a constrained temporal walk from the source.
Cite as

Filippo Brunelli and Laurent Viennot. Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 4:1-4:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{brunelli_et_al:LIPIcs.SAND.2023.4,
  author =	{Brunelli, Filippo and Viennot, Laurent},
  title =	{{Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{4:1--4:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.4},
  URN =		{urn:nbn:de:0030-drops-179402},
  doi =		{10.4230/LIPIcs.SAND.2023.4},
  annote =	{Keywords: temporal reachability, temporal graph, temporal path, temporal walk, waiting-time constraints, restless temporal walk, linear time}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.5
Complexity of Motion Planning of Arbitrarily Many Robots: Gadgets, Petri Nets, and Counter Machines

Authors: Joshua Ani, Michael Coulombe, Erik D. Demaine, Yevhenii Diomidov, Timothy Gomez, Dylan Hendrickson, and Jayson Lynch

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
We extend the motion-planning-through-gadgets framework to several new scenarios involving various numbers of robots/agents, and analyze the complexity of the resulting motion-planning problems. While past work considers just one robot or one robot per player, most of our models allow for one or more locations to spawn new robots in each time step, leading to arbitrarily many robots. In the 0-player context, where all motion is deterministically forced, we prove that deciding whether any robot ever reaches a specified location is undecidable, by representing a counter machine. In the 1-player context, where the player can choose how to move the robots, we prove equivalence to Petri nets, EXPSPACE-completeness for reaching a specified location, PSPACE-completeness for reconfiguration, and ACKERMANN-completeness for reconfiguration when robots can be destroyed in addition to spawned. Finally, we consider a variation on the standard 2-player context where, instead of one robot per player, we have one robot shared by the players, along with a ko rule to prevent immediately undoing the previous move. We prove this impartial 2-player game EXPTIME-complete.
Cite as

Joshua Ani, Michael Coulombe, Erik D. Demaine, Yevhenii Diomidov, Timothy Gomez, Dylan Hendrickson, and Jayson Lynch. Complexity of Motion Planning of Arbitrarily Many Robots: Gadgets, Petri Nets, and Counter Machines. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 5:1-5:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{ani_et_al:LIPIcs.SAND.2023.5,
  author =	{Ani, Joshua and Coulombe, Michael and Demaine, Erik D. and Diomidov, Yevhenii and Gomez, Timothy and Hendrickson, Dylan and Lynch, Jayson},
  title =	{{Complexity of Motion Planning of Arbitrarily Many Robots: Gadgets, Petri Nets, and Counter Machines}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{5:1--5:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.5},
  URN =		{urn:nbn:de:0030-drops-179414},
  doi =		{10.4230/LIPIcs.SAND.2023.5},
  annote =	{Keywords: Gadgets, robots, undecidability, Petri nets}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.6
Adaptive Collective Responses to Local Stimuli in Anonymous Dynamic Networks

Authors: Shunhao Oh, Dana Randall, and Andréa W. Richa

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
We develop a framework for self-induced phase changes in programmable matter in which a collection of agents with limited computational and communication capabilities can collectively perform appropriate global tasks in response to local stimuli that dynamically appear and disappear. Agents reside on graph vertices, where each stimulus is only recognized locally, and agents communicate via token passing along edges to alert other agents to transition to an Aware state when stimuli are present and an Unaware state when the stimuli disappear. We present an Adaptive Stimuli Algorithm that is robust to competing waves of messages as multiple stimuli change, possibly adversarially. Moreover, in addition to handling arbitrary stimulus dynamics, the algorithm can handle agents reconfiguring the connections (edges) of the graph over time in a controlled way. As an application, we show how this Adaptive Stimuli Algorithm on reconfigurable graphs can be used to solve the foraging problem, where food sources may be discovered, removed, or shifted at arbitrary times. We would like the agents to consistently self-organize, using only local interactions, such that if the food remains in a position long enough, the agents transition to a gather phase in which many collectively form a single large component with small perimeter around the food. Alternatively, if no food source has existed recently, the agents should undergo a self-induced phase change and switch to a search phase in which they distribute themselves randomly throughout the lattice region to search for food. Unlike previous approaches to foraging, this process is indefinitely repeatable, withstanding competing waves of messages that may interfere with each other. Like a physical phase change, microscopic changes such as the deletion or addition of a single food source trigger these macroscopic, system-wide transitions as agents share information about the environment and respond locally to get the desired collective response.
Cite as

Shunhao Oh, Dana Randall, and Andréa W. Richa. Adaptive Collective Responses to Local Stimuli in Anonymous Dynamic Networks. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{oh_et_al:LIPIcs.SAND.2023.6,
  author =	{Oh, Shunhao and Randall, Dana and Richa, Andr\'{e}a W.},
  title =	{{Adaptive Collective Responses to Local Stimuli in Anonymous Dynamic Networks}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.6},
  URN =		{urn:nbn:de:0030-drops-179424},
  doi =		{10.4230/LIPIcs.SAND.2023.6},
  annote =	{Keywords: Dynamic networks, adaptive stimuli, foraging, self-organizing particle systems, programmable matter}
}
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