Pub Date : 2024-04-13DOI: 10.1007/s11047-024-09981-6
Andreas Padalkin, Christian Scheideler, Daniel Warner
The amoebot model (Derakhshandeh et al. in: SPAA ACM, pp 220–222. https://doi.org/10.1145/2612669.2612712, 2014) has been proposed as a model for programmable matter consisting of tiny, robotic elements called amoebots. We consider the reconfigurable circuit extension (Feldmann et al. in J Comput Biol 29(4):317–343. https://doi.org/10.1089/cmb.2021.0363, 2022) of the geometric amoebot model that allows the amoebot structure to interconnect amoebots by so-called circuits. A circuit permits the instantaneous transmission of signals between the connected amoebots. In this paper, we examine the structural power of the reconfigurable circuits. We start with fundamental problems like the stripe computation problem where, given any connected amoebot structure S, an amoebot u in S, and some axis X, all amoebots belonging to axis X through u have to be identified. Second, we consider the global maximum problem, which identifies an amoebot at the highest possible position with respect to some direction in some given amoebot (sub)structure. A solution to this problem can be used to solve the skeleton problem, where a cycle of amoebots has to be found in the given amoebot structure which contains all boundary amoebots. A canonical solution to that problem can be used to come up with a canonical path, which provides a unique characterization of the shape of the given amoebot structure. Constructing canonical paths for different directions allows the amoebots to set up a spanning tree and to check symmetry properties of the given amoebot structure. The problems are important for a number of applications like rapid shape transformation, energy dissemination, and structural monitoring. Interestingly, the reconfigurable circuit extension allows polylogarithmic-time solutions to all of these problems.
阿米巴机器人模型(Derakhshandeh et al:SPAA ACM, pp 220-222. https://doi.org/10.1145/2612669.2612712, 2014)已被提出作为可编程物质的模型,该模型由被称为变形虫的微小机器人元件组成。我们考虑的是几何变形虫模型的可重构电路扩展(Feldmann 等人,载于:J Comput Biol 29(4):317-343. https://doi.org/10.1089/cmb.2021.0363, 2022),它允许变形虫结构通过所谓的电路将变形虫相互连接起来。电路允许在连接的变形虫之间瞬时传输信号。在本文中,我们将研究可重构电路的结构能力。我们从基本问题入手,如条纹计算问题,即给定任何连接的变形机器人结构 S、S 中的变形机器人 u 和某个轴 X,必须识别出通过 u 属于轴 X 的所有变形机器人。其次,我们考虑全局最大值问题,即在给定的阿米机器人(子)结构中,确定一个阿米机器人相对于某个方向的最高位置。这个问题的解可以用来解决骨架问题,即必须在给定的变形机器人结构中找到一个包含所有边界变形机器人的变形机器人循环。该问题的规范解可以用来得出规范路径,它为给定变形机器人结构的形状提供了唯一的特征。通过构建不同方向的典型路径,阿米机器人可以建立生成树,并检查给定阿米机器人结构的对称性。这些问题对于快速形状转换、能量传播和结构监测等许多应用都非常重要。有趣的是,可重构电路扩展允许对所有这些问题进行多对数时间求解。
{"title":"The structural power of reconfigurable circuits in the amoebot model","authors":"Andreas Padalkin, Christian Scheideler, Daniel Warner","doi":"10.1007/s11047-024-09981-6","DOIUrl":"https://doi.org/10.1007/s11047-024-09981-6","url":null,"abstract":"<p>The <i>amoebot model</i> (Derakhshandeh et al. in: SPAA ACM, pp 220–222. https://doi.org/10.1145/2612669.2612712, 2014) has been proposed as a model for programmable matter consisting of tiny, robotic elements called <i>amoebots</i>. We consider the <i>reconfigurable circuit extension</i> (Feldmann et al. in J Comput Biol 29(4):317–343. https://doi.org/10.1089/cmb.2021.0363, 2022) of the geometric amoebot model that allows the amoebot structure to interconnect amoebots by so-called <i>circuits</i>. A circuit permits the instantaneous transmission of signals between the connected amoebots. In this paper, we examine the structural power of the reconfigurable circuits. We start with fundamental problems like the <i>stripe computation problem</i> where, given any connected amoebot structure <i>S</i>, an amoebot <i>u</i> in <i>S</i>, and some axis <i>X</i>, all amoebots belonging to axis <i>X</i> through <i>u</i> have to be identified. Second, we consider the <i>global maximum problem</i>, which identifies an amoebot at the highest possible position with respect to some direction in some given amoebot (sub)structure. A solution to this problem can be used to solve the <i>skeleton problem</i>, where a cycle of amoebots has to be found in the given amoebot structure which contains all boundary amoebots. A canonical solution to that problem can be used to come up with a canonical path, which provides a unique characterization of the shape of the given amoebot structure. Constructing canonical paths for different directions allows the amoebots to set up a spanning tree and to check symmetry properties of the given amoebot structure. The problems are important for a number of applications like rapid shape transformation, energy dissemination, and structural monitoring. Interestingly, the reconfigurable circuit extension allows polylogarithmic-time solutions to all of these problems.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-11DOI: 10.1007/s11047-024-09986-1
Artiom Alhazov, Rudolf Freund, Sergiu Ivanov
Reaction systems are a model of computing aiming to formalize biochemistry by capturing the qualitative relations between the species, and explicitly discarding any accounts of multiplicity. From the point of view of the formal language theory, this situates them in the realm of set rewriting. In this work, we propose a series of extensions of reaction systems to use strings. These extensions form a spectrum in the sense that all of them honor the hallmark features of the original model: the threshold principle and the non-permanency principle. We thoroughly discuss the details of the structure and the behavior of these variants, and commence studying their expressive power by comparing them to some classic models of computing.
{"title":"On the spectrum between reaction systems and string rewriting","authors":"Artiom Alhazov, Rudolf Freund, Sergiu Ivanov","doi":"10.1007/s11047-024-09986-1","DOIUrl":"https://doi.org/10.1007/s11047-024-09986-1","url":null,"abstract":"<p>Reaction systems are a model of computing aiming to formalize biochemistry by capturing the qualitative relations between the species, and explicitly discarding any accounts of multiplicity. From the point of view of the formal language theory, this situates them in the realm of set rewriting. In this work, we propose a series of extensions of reaction systems to use strings. These extensions form a spectrum in the sense that all of them honor the hallmark features of the original model: the threshold principle and the non-permanency principle. We thoroughly discuss the details of the structure and the behavior of these variants, and commence studying their expressive power by comparing them to some classic models of computing.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The past decade has seen the emergence of Ising machines targeting hard combinatorial optimization problems by minimizing the Ising Hamiltonian with spins represented by continuous dynamical variables. However, capabilities of these machines at larger scales are yet to be fully explored. We introduce and investigate an almost-linear Ising machine, a machine based on a network of analog spins with piece-wise linear coupling. We show that such networks leverage the computational resource similar to that of the semidefinite positive relaxation of the Ising model. We estimate the expected performance of the almost-linear machine and benchmark it on a set of (left{ 0, 1right})-weighted graphs. We show that the running time of the investigated machine scales polynomially (linearly with the number of edges in the connectivity graph). As an example of the physical realization of the machine, we present a CMOS-compatible implementation comprising an array of vertices efficiently storing the continuous spins on charged capacitors and communicating externally via analog current.
{"title":"Scalable almost-linear dynamical Ising machines","authors":"Aditya Shukla, Mikhail Erementchouk, Pinaki Mazumder","doi":"10.1007/s11047-024-09983-4","DOIUrl":"https://doi.org/10.1007/s11047-024-09983-4","url":null,"abstract":"<p>The past decade has seen the emergence of Ising machines targeting hard combinatorial optimization problems by minimizing the Ising Hamiltonian with spins represented by continuous dynamical variables. However, capabilities of these machines at larger scales are yet to be fully explored. We introduce and investigate an almost-linear Ising machine, a machine based on a network of analog spins with piece-wise linear coupling. We show that such networks leverage the computational resource similar to that of the semidefinite positive relaxation of the Ising model. We estimate the expected performance of the almost-linear machine and benchmark it on a set of <span>(left{ 0, 1right})</span>-weighted graphs. We show that the running time of the investigated machine scales polynomially (linearly with the number of edges in the connectivity graph). As an example of the physical realization of the machine, we present a CMOS-compatible implementation comprising an array of vertices efficiently storing the continuous spins on charged capacitors and communicating externally via analog current.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-06DOI: 10.1007/s11047-024-09972-7
Abstract
We study the efficiency of the reaction systems in solving NP-complete problems. Due to the fact that standard reaction systems are qualitative, in order to accomplish our aim, in this paper we consider communicating reaction systems with direct communication extended with duration for resources and a mutual exclusion relation between reactions forbidding two reactions to be used in the same step, in parallel. We show that these systems, working in a non-deterministic way, are powerful enough to provide polynomial-time solutions to the subset sum and SAT problems. We consider a semi-uniform approach by constructing a system for each instance of the subset sum and SAT problems and embedding the parameters into the constructed systems.
摘要 我们研究了反应系统在解决 NP-完全问题时的效率。由于标准反应系统是定性的,为了实现我们的目标,本文考虑了通信反应系统,该系统具有直接通信功能,扩展了资源的持续时间,以及反应之间的互斥关系,禁止在同一步骤中并行使用两个反应。我们的研究表明,这些系统以非决定性方式工作,足以为子集求和与 SAT 问题提供多项式时间解决方案。我们考虑了一种半统一方法,即为子集和与 SAT 问题的每个实例构建一个系统,并将参数嵌入所构建的系统中。
{"title":"Solving subset sum and SAT problems by reaction systems","authors":"","doi":"10.1007/s11047-024-09972-7","DOIUrl":"https://doi.org/10.1007/s11047-024-09972-7","url":null,"abstract":"<h3>Abstract</h3> <p>We study the efficiency of the reaction systems in solving NP-complete problems. Due to the fact that standard reaction systems are qualitative, in order to accomplish our aim, in this paper we consider communicating reaction systems with direct communication extended with duration for resources and a mutual exclusion relation between reactions forbidding two reactions to be used in the same step, in parallel. We show that these systems, working in a non-deterministic way, are powerful enough to provide polynomial-time solutions to the subset sum and SAT problems. We consider a semi-uniform approach by constructing a system for each instance of the subset sum and SAT problems and embedding the parameters into the constructed systems.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-06DOI: 10.1007/s11047-023-09971-0
Abstract
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues. These modifications consist of an extension to 3D, the ability of tiles to form “flexible” bonds that allow bound tiles to rotate relative to each other, and allowing tiles of multiple shapes within the same system. We call this new model the STAM*, and we present a series of constructions within it that are capable of self-replicating behavior. Namely, the input seed assemblies to our STAM* systems can encode either “genomes” specifying the instructions for building a target shape, or can be copies of the target shape with instructions built in. A universal tile set exists for any target shape (at scale factor 2), and from a genome assembly creates infinite copies of the genome as well as the target shape. An input target structure, on the other hand, can be “deconstructed” by the universal tile set to form a genome encoding it, which will then replicate and also initiate the growth of copies of assemblies of the target shape. Since the lengths of the genomes for these constructions are proportional to the number of points in the target shape, we also present a replicator which utilizes hierarchical self-assembly to greatly reduce the size of the genomes required. The main goals of this work are to examine minimal requirements of self-assembling systems capable of self-replicating behavior, with the aim of better understanding self-replication in nature as well as understanding the complexity of mimicking it.
{"title":"Self-replication via tile self-assembly","authors":"","doi":"10.1007/s11047-023-09971-0","DOIUrl":"https://doi.org/10.1007/s11047-023-09971-0","url":null,"abstract":"<h3>Abstract</h3> <p>In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues. These modifications consist of an extension to 3D, the ability of tiles to form “flexible” bonds that allow bound tiles to rotate relative to each other, and allowing tiles of multiple shapes within the same system. We call this new model the STAM*, and we present a series of constructions within it that are capable of self-replicating behavior. Namely, the input seed assemblies to our STAM* systems can encode either “genomes” specifying the instructions for building a target shape, or can be copies of the target shape with instructions built in. A universal tile set exists for any target shape (at scale factor 2), and from a genome assembly creates infinite copies of the genome as well as the target shape. An input target structure, on the other hand, can be “deconstructed” by the universal tile set to form a genome encoding it, which will then replicate and also initiate the growth of copies of assemblies of the target shape. Since the lengths of the genomes for these constructions are proportional to the number of points in the target shape, we also present a replicator which utilizes hierarchical self-assembly to greatly reduce the size of the genomes required. The main goals of this work are to examine minimal requirements of self-assembling systems capable of self-replicating behavior, with the aim of better understanding self-replication in nature as well as understanding the complexity of mimicking it.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-29DOI: 10.1007/s11047-024-09978-1
Mariusz Kaniecki, Łukasz Mikulski
In every matured theory, there is a need to investigate possible relationships between considered objects. To address this issue, it is natural to relate a category with given model of computing. Thanks to such approach, many properties are unified and simplified. In this paper, we investigate how category theory can be used to give a faithful semantics for reaction systems. In particular, we propose and discuss possible approaches to the problem of defining morphisms between reaction systems. We provide the definition of morphism that keeps the behaviour of the original reaction system. Especially, some equivalences of reaction systems are reflected in terms of morphisms. For this purpose we expressed isomorphisms and sections in term of transition systems. Moreover, the accelerating morphism defined in the last section gives a new approach for including time in reaction systems.
{"title":"On categorical approach to reaction systems","authors":"Mariusz Kaniecki, Łukasz Mikulski","doi":"10.1007/s11047-024-09978-1","DOIUrl":"https://doi.org/10.1007/s11047-024-09978-1","url":null,"abstract":"<p>In every matured theory, there is a need to investigate possible relationships between considered objects. To address this issue, it is natural to relate a category with given model of computing. Thanks to such approach, many properties are unified and simplified. In this paper, we investigate how category theory can be used to give a faithful semantics for reaction systems. In particular, we propose and discuss possible approaches to the problem of defining morphisms between reaction systems. We provide the definition of morphism that keeps the behaviour of the original reaction system. Especially, some equivalences of reaction systems are reflected in terms of morphisms. For this purpose we expressed isomorphisms and sections in term of transition systems. Moreover, the accelerating morphism defined in the last section gives a new approach for including time in reaction systems.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140325382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-29DOI: 10.1007/s11047-024-09979-0
David Furcy, Scott M. Summers, Hailey Vadnais
We study the problem of determining the size of the smallest tile set that uniquely self-assembles into a given target shape in Winfree’s abstract Tile Assembly Model (aTAM), an elegant theoretical model of DNA tile self-assembly. This problem is also known as the “directed tile complexity” problem. We prove two main results related to the directed tile complexity problem within a variant of the aTAM in which the minimum binding strength threshold (temperature) is set to 1. For our first result, self-assembly happens in a “just-barely 3D” setting, where self-assembling unit cubes are allowed to be placed in the (z=0) and (z=1) planes. This is the same setting in which Furcy, Summers and Withers (DNA 2021) recently proved lower and upper bounds on the directed tile complexity of a just-barely 3D (k times N) rectangle at temperature 1 of (Omega left( N^{frac{1}{k}}right) ) and (Oleft( N^{frac{1}{k-1}}+log Nright) ), respectively, the latter of which does not hold for (k=2). Our first result closes this gap for (k=2) by proving an asymptotically tight bound of (Theta (N)) on the directed tile complexity of a just-barely 3D (2 times N) rectangle at temperature 1. Our proof uses a novel process by which a just-barely 3D assembly sequence is “unfolded” to an equivalent 2D assembly sequence. For our second result, we use the aforementioned lower bound by Furcy, Summers and Withers and a novel process that is complementary-in-spirit to our 3D-to-2D unfolding process, by which we “fold” a 2D tile assembly to an equivalent just-barely 3D assembly to prove a new lower bound on the directed tile complexity of a 2D (k times N) rectangle at temperature 1 of (Omega left( frac{N^{frac{2}{k + (k bmod 2)}}}{k} right) ). For fixed k, our new bound gives a nearly quadratic improvement over, and matches for general even values of (k < frac{log N}{log log N - log log log N}) the state of the art lower bound on the directed tile complexity of a (k times N) rectangle at temperature 1 by Furcy, Summers and Wendlandt (DNA 2019) of (Omega left( N^{frac{1}{k}}right) ). While both of our results represent improvements over previous corresponding state of the art results, the proofs thereof are facilitated by novel examples of reasoning about tile self-assembly happening in 2D (just-barely 3D) as though it is happening in just-barely 3D (2D).
{"title":"Proving new directed tile complexity lower bounds at temperature 1 by folding between 2D and just-barely 3D self-assembly","authors":"David Furcy, Scott M. Summers, Hailey Vadnais","doi":"10.1007/s11047-024-09979-0","DOIUrl":"https://doi.org/10.1007/s11047-024-09979-0","url":null,"abstract":"<p>We study the problem of determining the size of the smallest tile set that uniquely self-assembles into a given target shape in Winfree’s abstract Tile Assembly Model (aTAM), an elegant theoretical model of DNA tile self-assembly. This problem is also known as the “directed tile complexity” problem. We prove two main results related to the directed tile complexity problem within a variant of the aTAM in which the minimum binding strength threshold (temperature) is set to 1. For our first result, self-assembly happens in a “just-barely 3D” setting, where self-assembling unit cubes are allowed to be placed in the <span>(z=0)</span> and <span>(z=1)</span> planes. This is the same setting in which Furcy, Summers and Withers (DNA 2021) recently proved lower and upper bounds on the directed tile complexity of a just-barely 3D <span>(k times N)</span> rectangle at temperature 1 of <span>(Omega left( N^{frac{1}{k}}right) )</span> and <span>(Oleft( N^{frac{1}{k-1}}+log Nright) )</span>, respectively, the latter of which does not hold for <span>(k=2)</span>. Our first result closes this gap for <span>(k=2)</span> by proving an asymptotically tight bound of <span>(Theta (N))</span> on the directed tile complexity of a just-barely 3D <span>(2 times N)</span> rectangle at temperature 1. Our proof uses a novel process by which a just-barely 3D assembly sequence is “unfolded” to an equivalent 2D assembly sequence. For our second result, we use the aforementioned lower bound by Furcy, Summers and Withers and a novel process that is complementary-in-spirit to our 3D-to-2D unfolding process, by which we “fold” a 2D tile assembly to an equivalent just-barely 3D assembly to prove a new lower bound on the directed tile complexity of a 2D <span>(k times N)</span> rectangle at temperature 1 of <span>(Omega left( frac{N^{frac{2}{k + (k bmod 2)}}}{k} right) )</span>. For fixed <i>k</i>, our new bound gives a nearly quadratic improvement over, and matches for general even values of <span>(k < frac{log N}{log log N - log log log N})</span> the state of the art lower bound on the directed tile complexity of a <span>(k times N)</span> rectangle at temperature 1 by Furcy, Summers and Wendlandt (DNA 2019) of <span>(Omega left( N^{frac{1}{k}}right) )</span>. While both of our results represent improvements over previous corresponding state of the art results, the proofs thereof are facilitated by novel examples of reasoning about tile self-assembly happening in 2D (just-barely 3D) as though it is happening in just-barely 3D (2D).</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140325385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-15DOI: 10.1007/s11047-024-09977-2
Rocco Ascone, Giulia Bernardini, Luca Manzoni
Reaction systems are discrete dynamical systems that simulate biological processes within living cells through finite sets of reactants, inhibitors, and products. In this paper, we study the computational complexity of deciding on the existence of fixed points and attractors in the restricted class of additive reaction systems, in which each reaction involves at most one reactant and no inhibitors. We prove that all the considered problems, that are known to be hard for other classes of reaction systems, are polynomially solvable in additive systems. To arrive at these results, we provide several non-trivial reductions to problems on a polynomially computable graph representation of reaction systems that might prove useful for addressing other related problems in the future.
{"title":"Fixed points and attractors of additive reaction systems","authors":"Rocco Ascone, Giulia Bernardini, Luca Manzoni","doi":"10.1007/s11047-024-09977-2","DOIUrl":"https://doi.org/10.1007/s11047-024-09977-2","url":null,"abstract":"<p>Reaction systems are discrete dynamical systems that simulate biological processes within living cells through finite sets of reactants, inhibitors, and products. In this paper, we study the computational complexity of deciding on the existence of fixed points and attractors in the restricted class of additive reaction systems, in which each reaction involves at most one reactant and no inhibitors. We prove that all the considered problems, that are known to be hard for other classes of reaction systems, are polynomially solvable in additive systems. To arrive at these results, we provide several non-trivial reductions to problems on a polynomially computable graph representation of reaction systems that might prove useful for addressing other related problems in the future.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140154333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The use of Cellular Automata (CA) in combination with Learning Automata (LA) has demonstrated effectiveness in handling hard-to-be-solved problems. Due to their capacity to learn and adapt, as well as their inherent parallelism, they can expedite the problem-solving process for a range of problems, such as challenging logic puzzles. One such puzzle is Sudoku, which poses a combinatorial optimization challenge of great difficulty and complexity. In this study, a Sudoku puzzle was represented as an Irregular Learning Cellular Automaton (ILCA), using a reward and penalty algorithm to resolve it. Simulations for an amount of 400 puzzles were performed, while the results demonstrate that the proposed algorithm operates effectively, highlighting the concurrent and learning capabilities of the ILCA structure. Furthermore, two different performance enhancement methods are investigated, namely learning rates method and selective probability reset rule, which are able to increase the initial performance by (26.8%) and to achieve an overall (99.3%) resolution rate.
{"title":"Handling Sudoku puzzles with irregular learning cellular automata","authors":"Theodoros Panagiotis Chatzinikolaou, Rafailia-Eleni Karamani, Iosif-Angelos Fyrigos, Georgios Ch. Sirakoulis","doi":"10.1007/s11047-024-09975-4","DOIUrl":"https://doi.org/10.1007/s11047-024-09975-4","url":null,"abstract":"<p>The use of Cellular Automata (CA) in combination with Learning Automata (LA) has demonstrated effectiveness in handling hard-to-be-solved problems. Due to their capacity to learn and adapt, as well as their inherent parallelism, they can expedite the problem-solving process for a range of problems, such as challenging logic puzzles. One such puzzle is Sudoku, which poses a combinatorial optimization challenge of great difficulty and complexity. In this study, a Sudoku puzzle was represented as an Irregular Learning Cellular Automaton (ILCA), using a reward and penalty algorithm to resolve it. Simulations for an amount of 400 puzzles were performed, while the results demonstrate that the proposed algorithm operates effectively, highlighting the concurrent and learning capabilities of the ILCA structure. Furthermore, two different performance enhancement methods are investigated, namely learning rates method and selective probability reset rule, which are able to increase the initial performance by <span>(26.8%)</span> and to achieve an overall <span>(99.3%)</span> resolution rate.\u0000</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140098814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-25DOI: 10.1007/s11047-024-09974-5
Erzsébet Csuhaj-Varjú, György Vaszil
A distributed reaction system consists of a finite set of reaction systems that either interact with a common environment or interact with each other by communicating products or reactions. A reaction system is a well-known qualitative formal model of interactions between biochemical reactions. A reaction is a triplet of nonempty sets representing chemicals, called the set of reactants, the set of inhibitors, and the set of products. A reaction corresponds to a chemical reaction performed on a set of chemicals, and a reaction system is a finite nonempty set of reactions. In this paper, we examine two variants of distributed reaction systems. We introduce the notion of a distributed reaction system with communication by request (a qDRS for short), where sets of products are communicated between the component reaction systems by queries. First, we show that every qDRS can be represented by a reaction system. After that we compare distributed reaction systems with communication by request to extended distributed reaction systems (EDRSs), models that were introduced in a previous paper. We prove that extended distributed reaction systems, where a context automaton provides input for the component reaction systems, simulate distributed reaction systems with communication by request and distributed reaction systems with communication by request simulate special variants of extended distributed reaction systems. Furthermore, we assign languages to these two variants of distributed reaction systems. We prove that the class of agreement languages of extended distributed reaction systems is equal to the class of languages of nondeterministic multihead finite automata and the agreement language of every distributed reaction system with communication by request is an element of a certain subregular language class.
{"title":"Variants of distributed reaction systems","authors":"Erzsébet Csuhaj-Varjú, György Vaszil","doi":"10.1007/s11047-024-09974-5","DOIUrl":"https://doi.org/10.1007/s11047-024-09974-5","url":null,"abstract":"<p>A distributed reaction system consists of a finite set of reaction systems that either interact with a common environment or interact with each other by communicating products or reactions. A reaction system is a well-known qualitative formal model of interactions between biochemical reactions. A reaction is a triplet of nonempty sets representing chemicals, called the set of reactants, the set of inhibitors, and the set of products. A reaction corresponds to a chemical reaction performed on a set of chemicals, and a reaction system is a finite nonempty set of reactions. In this paper, we examine two variants of distributed reaction systems. We introduce the notion of a distributed reaction system with communication by request (a qDRS for short), where sets of products are communicated between the component reaction systems by queries. First, we show that every qDRS can be represented by a reaction system. After that we compare distributed reaction systems with communication by request to extended distributed reaction systems (EDRSs), models that were introduced in a previous paper. We prove that extended distributed reaction systems, where a context automaton provides input for the component reaction systems, simulate distributed reaction systems with communication by request and distributed reaction systems with communication by request simulate special variants of extended distributed reaction systems. Furthermore, we assign languages to these two variants of distributed reaction systems. We prove that the class of agreement languages of extended distributed reaction systems is equal to the class of languages of nondeterministic multihead finite automata and the agreement language of every distributed reaction system with communication by request is an element of a certain subregular language class.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139978315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}