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Natural Computing OnlineFirst articles

Open Access 15-03-2024

Fixed points and attractors of additive reaction systems

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 …

Authors:
Rocco Ascone, Giulia Bernardini, Luca Manzoni

Open Access 25-02-2024

Variants of distributed reaction systems

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 …

Authors:
Erzsébet Csuhaj-Varjú, György Vaszil

24-02-2024

Ranks of functions specified by minimal reaction systems and induced by images of singletons

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 …

Authors:
Husain Intekhab, Wen Chean Teh

21-09-2023

Parallel pairwise operations on data stored in DNA: sorting, XOR, shifting, and searching

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 …

Authors:
Arnav Solanki, Tonglin Chen, Marc Riedel

26-04-2023

Fractal dimension of assemblies in the abstract tile assembly model

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 …

Authors:
Daniel Hader, Matthew J. Patitz, Scott M. Summers

25-03-2023

A reversible system based on hybrid toggle radius-4 cellular automata and its application as a block cipher

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 …

Authors:
Everton R. Lira, Heverton B. de Macêdo, Danielli A. Lima, Leonardo Alt, Gina M. B. Oliveira

Open Access 17-01-2023

Population diversity and inheritance in genetic programming for symbolic regression

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 …

Authors:
Bogdan Burlacu, Kaifeng Yang, Michael Affenzeller

12-01-2023

Models to classify the difficulty of genetic algorithms to solve continuous optimization problems

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 …

Authors:
Noel E. Rodríguez-Maya, Juan J. Flores, Sébastien Verel, Mario Graff

10-01-2023

Gravitationally invariant subspaces in quantum computing

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 …

Authors:
Tanner Crowder, Marco Lanzagorta

Open Access 06-01-2023

Information theoretical properties of a spiking neuron trained with Hebbian and STDP learning rules

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 …

Author:
Dominique Chu

29-12-2022

A frequency-based parent selection for reducing the effect of evaluation time bias in asynchronous parallel multi-objective evolutionary algorithms

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 …

Author:
Tomohiro Harada

15-12-2022

CA-NN: a cellular automata neural network for handwritten pattern recognition

Convolutional neural networks (CNNs) are best suited for image data. The most important layer in CNNs is the convolution layer. In this paper, cellular automata neural network or CA-NN is proposed for handwritten pattern recognition that replaces …

Author:
Aamir Wali

08-10-2022

Self-organizing nest migration dynamics synthesis for ant colony systems

In this study, we synthesize a novel dynamical approach for ant colonies enabling them to migrate to new nest sites in a self-organizing fashion. In other words, we realize ant colony migration as a self-organizing phenotype-level collective …

Author:
Matin Macktoobian

08-09-2022

Is integration of mechanisms a way to enhance a nature-inspired algorithm?

A lot of discussion is done these days regarding the actual novelty of newcomer nature-inspired approaches. Crucial role on that matter is played by the mechanisms included in these approaches, where many of these mechanisms have been previously …

Authors:
Marios Thymianis, Alexandros Tzanetos

11-08-2022

A self-adaptive evolutionary algorithm using Monte Carlo Fragment insertion and conformation clustering for the protein structure prediction problem

The Protein Structure Prediction Problem is one of the most important and challenging open problems in Computer Science and Structural Bioinformatics. Accurately predicting protein conformations would significantly impact several fields, such as …

Authors:
Rafael Stubs Parpinelli, Nilcimar Neitzel Will, Renan Samuel da Silva

Open Access 22-02-2022

Turning machines: a simple algorithmic model for molecular robotics

Molecular robotics is challenging, so it seems best to keep it simple. We consider an abstract molecular robotics model based on simple folding instructions that execute asynchronously. Turning Machines are a simple 1D to 2D folding model, also …

Authors:
Irina Kostitsyna, Cai Wood, Damien Woods

21-01-2022

ALCH: An imperative language for chemical reaction network-controlled tile assembly

Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals …

Authors:
Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley

17-11-2021

Verification and computation in restricted Tile Automata

Many models of self-assembly have been shown to be capable of performing computation. Tile Automata was recently introduced combining features of both Cellular Automata and the 2-Handed Model of self-assembly both capable of universal computation.

Authors:
David Caballero, Timothy Gomez, Robert Schweller, Tim Wylie

17-11-2021

Population-induced phase transitions and the verification of chemical reaction networks

We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use …

Authors:
James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, Matthew R. Riley

06-07-2011

Topological active volume 3D segmentation model optimized with genetic approaches

The topological active volumes is an active model focused on 3D segmentation tasks. It is based on the 2D Topological Active Nets model and provides information about the surfaces and the inside of the detected objects in the scene. This paper …

Authors:
Jorge Novo, Noelia Barreira, Manuel González Penedo, José Santos