Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Boolean networks at the critical point have been a matter of debate for many years as, e.g., the scaling of numbers of attractors with system size. Recently it was found that this number scales superpolynomially with system size, contrary to a common earlier expectation of sublinear scaling. We point out here that these results are obtained using deterministic parallel update, where a large fraction of attractors are an artifact of the updating scheme. This limits the significance of these results for biological systems where noise is omnipresent. Here we take a fresh look at attractors in Boolean networks with the original motivation of simplified models for biological systems in mind. We test the stability of attractors with respect to infinitesimal deviations from synchronous update and find that most attractors are artifacts arising from synchronous clocking. The remaining fraction of attractors are stable against fluctuating delays. The average number of these stable attractors grows sublinearly with system size in the numerically tractable range.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1103/PhysRevE.72.055101 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Phenomenological modeling of gene transcription by approximating cooperativity of transcription factors improves prediction and reduces complexity in gene regulatory network models.
J Theor Biol
September 2025
Department of Bioengineering, Indian Institute of Science, Bengaluru 560012, India. Electronic address:
Several computational models are available for representing the gene expression process, with each having their advantages and disadvantages. Phenomenological models are widely used as they make appropriate simplifications that aim to find a middle ground between accuracy and complexity. The existing phenomenological models compete in terms of how the transcription initiation process is approximated, to achieve high accuracy while having the lowest complexity possible.
View Article and Find Full Text PDFExploring the interplay between circadian rhythms and obesity: A Boolean network approach to understanding metabolic dysregulation.
PLoS One
September 2025
Department of Biological Sciences, University of Limerick, Limerick, Ireland.
This study investigates the interaction between circadian rhythms and lipid metabolism disruptions in the context of obesity. Obesity is known to interfere with daily rhythmicity, a crucial process for maintaining brain homeostasis. To better understand this relationship, we analyzed transcriptional data from mice fed with normal or high-fat diet, focusing on the mechanisms linking genes involved with those regulating circadian rhythms.
View Article and Find Full Text PDFCombining greedy and evolutionary algorithms to maximize influence in networks under deterministic linear threshold model.
PLoS One
September 2025
Information Technologies and Programming Faculty, ITMO University, Saint Petersburg, Russia.
In the paper we consider the well-known Influence Maximization (IM) and Target Set Selection (TSS) problems for Boolean networks under Deterministic Linear Threshold Model (DLTM). The main novelty of our paper is that we state these problems in the context of pseudo-Boolean optimization and solve them using evolutionary algorithms in combination with the known greedy heuristic. We also propose a new variant of (1 + 1)-Evolutionary Algorithm, which is designed to optimize a fitness function on the subset of the Boolean hypercube comprised of vectors of a fixed Hamming weight.
View Article and Find Full Text PDFIntegration of Democratic Values in Natural Sciences Education: a Review of the Literature of the Last 50 Years.
F1000Res
September 2025
Faculty of Education, Universidad de La Sabana, Chía, Cundinamarca, Colombia.
This study examines how democratic values have been promoted through natural sciences education over the last 50 years, providing a comprehensive analysis based on a systematic review of relevant literature. The central problem addressed is understanding the role of natural science education in fostering democratic values such as equity, participation, critical thinking, and ethical responsibility. This research aims to identify and analyze strategies, methodologies, and transformative experiences that contribute to the promotion of democratic values.
View Article and Find Full Text PDFGeneralization power of threshold Boolean networks.
Biosystems
August 2025
Escuela de Ingeniería, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile. Electronic address:
Threshold Boolean networks are widely used to model gene regulatory systems and social dynamics such as consensus formation. In these networks, each node takes a binary value (0 or 1), leading to an exponential growth in the number of possible configurations with the number of nodes (2). Inferring such networks involves learning a weight matrix and threshold vector from configuration data.
View Article and Find Full Text PDF