BACKGROUND: Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors-subsets of the state space towards which the BN eventually converges. These are then typically linked to different biological phenotypes. Depending on various logical parameters, the structure and quality of attractors can undergo a significant change, known as a bifurcation. We present a methodology for analysing bifurcations in asynchronous parametrised Boolean networks. RESULTS: In this paper, we propose a computational framework employing advanced symbolic graph algorithms that enable the analysis of large networks with hundreds of Boolean variables. To visualise the results of this analysis, we developed a novel interactive presentation technique based on decision trees, allowing us to quickly uncover parameters crucial to the changes in the attractor landscape. As a whole, the methodology is implemented in our tool AEON. We evaluate the method's applicability on a complex human cell signalling network describing the activity of type-1 interferons and related molecules interacting with SARS-COV-2 virion. In particular, the analysis focuses on explaining the potential suppressive role of the recently proposed drug molecule GRL0617 on replication of the virus. CONCLUSIONS: The proposed method creates a working analogy to the concept of bifurcation analysis widely used in kinetic modelling to reveal the impact of parameters on the system's stability. The important feature of our tool is its unique capability to work fast with large-scale networks with a relatively large extent of unknown information. The results obtained in the case study are in agreement with the recent biological findings.

• Klíčová slova
• Attractor bifurcation, Boolean networks, Software tool, Symbolic computation, type-1 interferons,
• MeSH
• algoritmy MeSH
• aniliny MeSH
• benzamidy MeSH
• COVID-19 * MeSH
• genové regulační sítě * MeSH
• lidé MeSH
• modely genetické MeSH
• naftaleny MeSH
• SARS-CoV-2 MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 5-amino-2-methyl-N-((R)-1-(1-naphthyl)ethyl)benzamide MeSH Prohlížeč
• aniliny MeSH
• benzamidy MeSH
• naftaleny MeSH

Investigating the effect of changes in neuronal connectivity on the brain's behavior is of interest in neuroscience studies. Complex network theory is one of the most capable tools to study the effects of these changes on collective brain behavior. By using complex networks, the neural structure, function, and dynamics can be analyzed. In this context, various frameworks can be used to mimic neural networks, among which multi-layer networks are a proper one. Compared to single-layer models, multi-layer networks can provide a more realistic model of the brain due to their high complexity and dimensionality. This paper examines the effect of changes in asymmetry coupling on the behaviors of a multi-layer neuronal network. To this aim, a two-layer network is considered as a minimum model of left and right cerebral hemispheres communicated with the corpus callosum. The chaotic model of Hindmarsh-Rose is taken as the dynamics of the nodes. Only two neurons of each layer connect two layers of the network. In this model, it is assumed that the layers have different coupling strengths, so the effect of each coupling change on network behavior can be analyzed. As a result, the projection of the nodes is plotted for several coupling strengths to investigate how the asymmetry coupling influences the network behaviors. It is observed that although no coexisting attractor is present in the Hindmarsh-Rose model, an asymmetry in couplings causes the emergence of different attractors. The bifurcation diagrams of one node of each layer are presented to show the variation of the dynamics due to coupling changes. For further analysis, the network synchronization is investigated by computing intra-layer and inter-layer errors. Calculating these errors shows that the network can be synchronized only for large enough symmetric coupling.

• Klíčová slova
• asymmetry coupling, attractor, multi-layer networks, neuronal network, synchronization,
• MeSH
• modely neurologické MeSH
• mozek * fyziologie   MeSH
• neuronové sítě (počítačové) MeSH
• neurony * fyziologie   MeSH
• shluková analýza MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We examine experimentally a chemical system in a flow-through stirred reactor, which is known to provide large-amplitude oscillations of the pH value. By systematic variation of the flow rate, we find that the system displays hysteresis between a steady state and oscillations, and more interestingly, a transition to chaos involving mixed-mode oscillations. The basic pattern of the measured pH in the mixed-mode regime includes a large-scale peak followed by a series of oscillations on a much smaller scale, which are usually highly irregular and of variable duration. The bifurcation diagram shows that chaos sets in via a period-doubling route observed on the large-amplitude scale, but simultaneously small-amplitude oscillations are involved. Beyond the apparent accumulation of period doubling bifurcations, a mixed-mode regime with irregular oscillations on both scales is observed, occasionally interrupted by windows of periodicity. As the flow rate is further increased, chaos turns into quasiperiodicity and later to a simple small-amplitude periodic regime. Dynamics of selected typical regimes were examined with the tools of nonlinear time-series analysis, which include phase space reconstruction of an attractor and calculation of the maximal Lyapunov exponent. The analysis points to deterministic chaos, which appears via a period doubling route from below and via a route involving quasiperiodicity from above, when the flow rate is varied.

• Publikační typ
• časopisecké články MeSH

Studying simple chaotic systems with fractional-order derivatives improves modeling accuracy, increases complexity, and enhances control capabilities and robustness against noise. This paper investigates the dynamics of the simple Sprott-B chaotic system using fractional-order derivatives. This study involves a comprehensive dynamical analysis conducted through bifurcation diagrams, revealing the presence of coexisting attractors. Additionally, the synchronization behavior of the system is examined for various derivative orders. Finally, the integer-order and fractional-order electronic circuits are implemented to validate the theoretical findings. This research contributes to a deeper understanding of the Sprott-B system and its fractional-order dynamics, with potential applications in diverse fields such as chaos-based secure communications and nonlinear control systems.

• Klíčová slova
• Sprott-B system, circuit implementation, dynamical analysis, fractional order,
• Publikační typ
• časopisecké články MeSH

The objective of this paper is the study of the dynamical properties analysis of an original specification of the classical Cournot heterogeneous model with optimal response; specifically, a new approach that considers ordinal utility instead of cardinal monetary amounts is proposed where the classical decision of quantity is disentangled from the decision on imitation. The analysis is performed by means of bifurcation diagrams, the 0-1 test for chaos, power spectral density, histograms, and trajectory analysis. For this purpose, a new perturbation parameter ε of the initial condition is introduced, and together with the intensity of choice parameter β determining the share of responders vs imitators, the system is researched. Depending on ε and β, extreme reach dynamics, and coexisting attractors, periodic and chaotic trajectories are investigated through massive simulations. Those dynamics represent alternation between stability, cycles and chaos in the market. As the dynamics are completely endogenous, it means that swings in economy are intrinsic to the system and that they may persist unless controlled.

• MeSH
• nelineární dynamika * MeSH
• Publikační typ
• časopisecké články MeSH