scholarly journals Stochastic comparison of synchronization in activator- and repressor-based coupled gene oscillators

2021 ◽  
Author(s):  
Supravat Dey ◽  
A B M Shamim Ul Hasan ◽  
Abhyudai Singh ◽  
Hiroyuki Kurata
Keyword(s):  
Time Delay ◽  
Coupled Oscillators ◽  
Molecular Mechanisms ◽  
Phase Synchronization ◽  
Stochastic Comparison ◽  
Intercellular Coupling ◽  
Coupled Models ◽  
Coupling Delay ◽  
Coupling Time ◽  
Presence And Absence

Inside living cells, proteins or mRNA can show oscillations even without a periodic driving force. Such genetic oscillations are precise timekeepers for cell-cycle regulations, pattern formation during embryonic development in higher animals, and daily cycle maintenance in most organisms. The synchronization between oscillations in adjacent cells happens via intercellular coupling, which is essential for periodic segmentation formation in vertebrates and other biological processes. While molecular mechanisms of generating sustained oscillations are quite well understood, how do simple intercellular coupling produces robust synchronizations are still poorly understood? To address this question, we investigate two models of coupled gene oscillators - activator-based coupled oscillators (ACO) and repressor-based coupled oscillators (RCO) models. In our study, a single autonomous oscillator (that operates in a single cell) is based on a negative feedback, which is delayed by intracellular dynamics of an intermediate species. For the ACO model (RCO), the repressor protein of one cell activates (represses) the production of another protein in the neighbouring cell after a intercellular time delay. We investigate the coupled models in the presence of intrinsic noise due to the inherent stochasticity of the biochemical reactions. We analyze the collective oscillations from stochastic trajectories in the presence and absence of explicit coupling delay and make careful comparison between two models. Our results show no clear synchronizations in the ACO model when the coupling time delay is zero. However, a non-zero coupling delay can lead to anti-phase synchronizations in ACO. Interestingly, the RCO model shows robust in-phase synchronizations in the presence and absence of the coupling time delay. Our results suggest that the naturally occurring intercellular couplings might be based on repression rather than activation where in-phase synchronization is crucial.

TWOFOLD IMPACT OF DELAYED FEEDBACK ON COUPLED OSCILLATORS

2007 ◽  
Vol 17 (07) ◽  
pp. 2517-2530 ◽  
Author(s):  
OLEKSANDR V. POPOVYCH ◽  
VALERII KRACHKOVSKYI ◽  
PETER A. TASS
Keyword(s):  
Time Delay ◽  
Coupling Strength ◽  
Coupled Oscillators ◽  
Phase Synchronization ◽  
Threshold Value ◽  
Phase Oscillators ◽  
Intermediate Coupling ◽  
Rich Variety ◽  
Dynamical Regimes ◽  
The Impact

We present a detailed bifurcation analysis of desynchronization transitions in a system of two coupled phase oscillators with delay. The coupling between the oscillators combines a delayed self-feedback of each oscillator with an instantaneous mutual interaction. The delayed self-feedback leads to a rich variety of dynamical regimes, ranging from phase-locked and periodically modulated synchronized states to chaotic phase synchronization and desynchronization. We show that an increase of the coupling strength between oscillators may lead to a loss of synchronization. Intriguingly, the delay has a twofold influence on the oscillations: synchronizing for small and intermediate coupling strength and desynchronizing if the coupling strength exceeds a certain threshold value. We show that the desynchronization transition has the form of a crisis bifurcation of a chaotic attractor of chaotic phase synchronization. This study contributes to a better understanding of the impact of time delay on interacting oscillators.

scholarly journals Unique Patterns of Mating Pheromone Presence and Absence could Result in the Ambiguous Sexual Behaviours of Colletotrichum Species

2020 ◽  
Author(s):  
Andrea Melissa Wilson ◽  
RV Lelwala ◽  
PWJ Taylor ◽  
MJ Wingfield ◽  
BD WINGFIELD
Keyword(s):  
Mating Type ◽  
Molecular Mechanisms ◽  
Mating Strategies ◽  
Mating Partner ◽  
Filamentous Ascomycete ◽  
Sexual Behaviours ◽  
History Of ◽  
Ascomycete Fungi ◽  
Presence And Absence ◽  
Sexual Progeny

Abstract Background: Colletotrichum species are known to engage in unique sexual behaviours that differ significantly from the mating strategies of other filamentous ascomycete species. Most ascomycete fungi require the expression of both the MAT1-1-1 and MAT1-2-1 genes to regulate mating type and induce sexual reproduction. In contrast, all isolates of Colletotrichum are known to harbour only the MAT1-2-1 gene and yet, are capable of recognizing suitable mating partners and producing sexual progeny. The molecular mechanisms contributing to mating types and behaviours in Colletotrichum are thus unknown. Results: A comparative genomics approach analysing genomes from 47 Colletotrichum isolates was used to elucidate a putative molecular mechanism underlying the unique sexual behaviours observed in Colletotrichum species. The existence of only the MAT1-2 idiomorph was confirmed across all species included in this study. Comparisons at the loci harbouring the two mating pheromones and their cognate receptors revealed interesting patterns of gene presence and absence as well as gene loss. The results also showed that these genes have been lost multiple times over the evolutionary history of this genus. Conclusion: The multiple losses of the pheromone genes in these species suggest strong selection against the typical mating strategies seen in other species. This further suggests that these pheromones no longer play a role in mating type determination and that the species of this genus have undiscovered mechanisms by which to control mating type and mating partner recognition. This research thus provides a base from which further interrogation of this topic can take place.

scholarly journals On the General Consensus Protocol in Multiagent Networks with Double-Integrator Dynamics and Coupling Time Delay

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Tao Dong ◽  
Xiaofeng Liao
Keyword(s):  
Time Delay ◽  
Matrix Theory ◽  
Sufficient Conditions ◽  
Consensus Algorithm ◽  
Directed Network ◽  
Consensus Protocol ◽  
Special Cases ◽  
Coupling Time ◽  
Almost All ◽  
Double Integrator

This paper considers the problem of the convergence of the consensus algorithm for multiple agents in a directed network where each agent is governed by double-integrator dynamics and coupling time delay. The advantage of this protocol is that almost all the existing linear local interaction consensus protocols can be considered as special cases of the present paper. By combining algebraic graph theory and matrix theory and studying the distribution of the eigenvalues of the associated characteristic equation, some necessary and sufficient conditions are derived for reaching the second-order consensus. Finally, an illustrative example is also given to support the theoretical results.

PHASE SYNCHRONIZATION OF LINEARLY AND NONLINEARLY COUPLED OSCILLATORS WITH INTERNAL RESONANCE

2009 ◽  
Vol 23 (30) ◽  
pp. 5715-5726
Author(s):  
YONG LIU
Keyword(s):  
Coupling Strength ◽  
Coupled Oscillators ◽  
Internal Resonance ◽  
Natural Frequencies ◽  
Phase Synchronization ◽  
Coupled Systems ◽  
Nonlinear Coupling ◽  
Linear Coupling ◽  
Phase Dynamics ◽  
Diffuse Clouds

Phase synchronization between linearly and nonlinearly coupled systems with internal resonance is investigated in this paper. By introducing the conception of phase for a chaotic motion, it demonstrates that the detuning parameter σ between the two natural frequencies ω1and ω2affects phase dynamics, and with the increase in the linear coupling strength, the effect of phase synchronization between two sub-systems was enhanced, while increased firstly, and then decayed as nonlinear coupling strength increases. Further investigation reveals that the transition of phase states between the two oscillators are related to the critical changes of the Lyapunov exponents, which can also be explained by the diffuse clouds.

scholarly journals Synchronization Control of Time-Varying Complex Dynamic Network with Nonidentical Nodes and Coupling Time-Delay

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Youjian Zhang ◽  
Wenjun Yan ◽  
Qiang Yang
Keyword(s):  
Time Delay ◽  
Feedback Control ◽  
Complex Networks ◽  
Hybrid Control ◽  
Dynamic Network ◽  
Time Varying ◽  
Static Feedback ◽  
Control Schemes ◽  
Coupling Time ◽  
Nonidentical Nodes

This paper addresses the synchronization problem for a class of complex networks with time-varying topology as well as nonidentical nodes and coupling time-delay and presents two efficient control schemes to synchronize the network onto any given smooth goal dynamics. The time-varying network is supposed to be bounded within a certain range, which cannot be controlled. Through the adoption of hybrid control with linear static feedback control and adaptive feedback control, two control schemes are derived to guarantee such complex networks to reach the global synchronization. Finally, a set of numerical simulation experiments are carried out and the results demonstrate the effectiveness of the suggested control solutions.

scholarly journals Phase synchronization in time-delay systems

2006 ◽  
Vol 74 (3) ◽  
Author(s):  
D. V. Senthilkumar ◽  
M. Lakshmanan ◽  
J. Kurths
Keyword(s):  
Time Delay ◽  
Phase Synchronization ◽  
Delay Systems ◽  
Time Delay Systems

scholarly journals Controlling chaos in some laser systems via variable coupling and feedback time delays

2016 ◽  
Vol 30 (25) ◽  
pp. 1650181 ◽  
Author(s):  
E. M. Shahverdiev
Keyword(s):  
Time Delay ◽  
Feedback Loop ◽  
Pump Current ◽  
Bragg Reflector ◽  
Control Of Chaos ◽  
Distributed Bragg Reflector ◽  
Laser Systems ◽  
Coupling Time ◽  
Feedback Time ◽  
Variable Coupling

We study numerically a system of two lasers cross-coupled optoelectronically with a time delay where the output intensity of each laser modulates the pump current of the other laser. We demonstrate control of chaos via variable coupling time delay by converting the laser intensity chaos to the steady-state. We also show that wavelength chaos in an electrically tunable distributed Bragg reflector (DBR) laser diode with a feedback loop that can be controlled via variable feedback time delay.

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