Chemical reaction networks (CRNs) are an important tool for molecular programming. This field is rapidly expanding our ability to deploy computer programs into biological systems for various applications. However, CRNs are also difficult to work …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

This paper studies mathematical properties of reaction systems, which is a formal model introduced by Ehrenfeucht and Rozenberg and inspired by biochemical reactions that occur in living cells. Numerous studies have focused on reaction system …

Prior research has introduced the Single-Instruction-Multiple-Data paradigm for DNA computing (SIMD DNA). It offers the potential for storing information and performing in-memory computations on DNA, with massive parallelism. This paper introduces …

In this paper, we investigate the power of systems in the abstract Tile Assembly Model (aTAM) to self-assemble shapes having fractal dimensions between 1 and 2. We introduce the concept of sparsity as a tool for investigating such systems and …

The one-dimensional cellular automata (CA) system detailed herein uses a hybrid mechanism to attain reversibility, and this approach is adapted to create a novel block cipher algorithm called HCA (Hybrid Cellular Automata). CA are widely used for …

In this work we aim to empirically characterize two important dynamical aspects of GP search: the evolution of diversity and the propagation of inheritance patterns. Diversity is calculated at the genotypic and phenotypic levels using efficient …

What constitutes a hard optimization problem to an Evolutionary Algorithm (EA)? To answer the question, the study of Fitness Landscape (FL) has emerged as one of the most successful techniques. FL measures the landscape depicted by the problem’s …

Quantum information systems are fragile and highly susceptible to the deleterious effects of environmental noise. One noise source is due to the direct coupling of a massive spin-based quantum system and classical gravitational fields, which will …

Using formal methods complemented by large-scale simulations we investigate information theoretical properties of spiking neurons trained using Hebbian and STDP learning rules. It is shown that weight space contains meta-stable states, which are …

Parallel evolutionary algorithms (PEAs) have been studied for reducing the execution time of evolutionary algorithms by utilizing parallel computing. An asynchronous PEA (APEA) is a scheme of PEAs that increases computational efficiency by …