scholarly journals Coupling and noise in the circadian clock synchronization

2018 ◽  
Author(s):  
Marco A Herrera-Valdez ◽  
Pablo Padilla-Longoria ◽  
Alessio Franci ◽  
Miguel Lara-Aparicio
Keyword(s):  
Circadian Clock ◽  
Coupling Strength ◽  
Coupled Oscillators ◽  
Clock Synchronization ◽  
Nonlinear Models ◽  
Biological Rhythms ◽  
Planck Equation ◽  
General Purpose ◽  
Coupled Oscillations ◽  
Do So

The general purpose of this paper is to build up on our understanding of the basic mathematical principles that underlie the emergence of biological rhythms, in particular, the circadian clock. To do so, we study the role that the coupling strength and noise play in the synchronization of a system of nonlinear, linearly coupled oscillators. First, we study a deterministic version of the model to find plausible regions in the parameter space for which synchronization is observed. Second, we focus on studying how noise and coupling interact in determining the synchronized behavior. To do so, we leverage the Fokker-Planck equation associated with the system. The basic mechanisms behind the generation of oscillations and the emergence of synchrony that we describe here can be used as a guide to further study coupled oscillations in biophysical nonlinear models.

scholarly journals Synchronization, oscillator death, and frequency modulation in a class of biologically inspired coupled oscillators

2018 ◽  
Author(s):  
Alessio Franci ◽  
Marco A Herrera-Valdez ◽  
Miguel Lara-Aparicio ◽  
Pablo Padilla-Longoria
Keyword(s):  
Circadian Clock ◽  
Coupled Oscillators ◽  
Deterministic Model ◽  
Nonlinear Models ◽  
Biological Rhythms ◽  
Planck Equation ◽  
General Mechanism ◽  
Synchronous Oscillation ◽  
Synchronous Oscillations ◽  
Do So

The general purpose of this paper is to build up on our understanding of the basic mathematical principles that underlie the emergence of synchronous biological rhythms, in particular, the circadian clock. To do so, we study the role that the coupling strength, coupling type, and noise play in the synchronization of a system of coupled, nonlinear oscillators. First, we study a deterministic model based on Van der Pol coupled oscillators, modeling a population of diffusively coupled cells, to find regions in the parameter space for which synchronous oscillations emerge and to provide conditions under which diffusive coupling kills the synchronous oscillation. Second, we study how noise and coupling interact and lead to synchronous oscillations in linearly coupled oscillators, modeling the interaction between various pacemaker populations, each having an endogenous circadian clock. To do so, we use the Fokker-Planck equation associated to the system. We show how coupling can tune the frequency of the emergent synchronous oscillation, which provides a general mechanism to make fast (ultradian) pacemakers slow (circadian) and synchronous via coupling. The basic mechanisms behind the generation of oscillations and the emergence of synchrony that we describe here can be used to guide further studies of coupled oscillations in biophysical nonlinear models.

scholarly journals Synchronization, oscillator death, and frequency modulation in a class of biologically inspired coupled oscillators

2018 ◽  
Author(s):  
Alessio Franci ◽  
Marco A Herrera-Valdez ◽  
Miguel Lara-Aparicio ◽  
Pablo Padilla-Longoria
Keyword(s):  
Circadian Clock ◽  
Coupled Oscillators ◽  
Deterministic Model ◽  
Nonlinear Models ◽  
Biological Rhythms ◽  
Planck Equation ◽  
General Mechanism ◽  
Synchronous Oscillation ◽  
Synchronous Oscillations ◽  
Do So

The general purpose of this paper is to build up on our understanding of the basic mathematical principles that underlie the emergence of synchronous biological rhythms, in particular, the circadian clock. To do so, we study the role that the coupling strength, coupling type, and noise play in the synchronization of a system of coupled, nonlinear oscillators. First, we study a deterministic model based on Van der Pol coupled oscillators, modeling a population of diffusively coupled cells, to find regions in the parameter space for which synchronous oscillations emerge and to provide conditions under which diffusive coupling kills the synchronous oscillation. Second, we study how noise and coupling interact and lead to synchronous oscillations in linearly coupled oscillators, modeling the interaction between various pacemaker populations, each having an endogenous circadian clock. To do so, we use the Fokker-Planck equation associated to the system. We show how coupling can tune the frequency of the emergent synchronous oscillation, which provides a general mechanism to make fast (ultradian) pacemakers slow (circadian) and synchronous via coupling. The basic mechanisms behind the generation of oscillations and the emergence of synchrony that we describe here can be used to guide further studies of coupled oscillations in biophysical nonlinear models.

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.

FREQUENCY SYNCHRONIZATION IN NETWORKS OF COUPLED OSCILLATORS, A MONOTONE DYNAMICAL SYSTEMS APPROACH

2009 ◽  
Vol 19 (12) ◽  
pp. 4107-4116 ◽  
Author(s):  
WEN-XIN QIN
Keyword(s):  
Dynamical Systems ◽  
Coupling Strength ◽  
Coupled Oscillators ◽  
Systems Approach ◽  
System Size ◽  
Coupling Scheme ◽  
Frequency Synchronization ◽  
Nonlinear Coupling ◽  
New Approach ◽  
Monotone Dynamical Systems

We propose a new approach to investigate the frequency synchronization in networks of coupled oscillators. By making use of the theory of monotone dynamical systems, we show that frequency synchronization occurs in networks of coupled oscillators, provided the coupling scheme is symmetric, connected, and strongly cooperative. Our criterion is independent of the system size, the coupling strength and the details of the connections, and applies also to nonlinear coupling schemes.

ByShard

2021 ◽  
Vol 14 (11) ◽  
pp. 2230-2243
Author(s):  
Jelle Hellings ◽  
Mohammad Sadoghi
Keyword(s):  
Data Management ◽  
Phase Locking ◽  
Large Data ◽  
General Purpose ◽  
Management Systems ◽  
Two Phase ◽  
Data Management Systems ◽  
Malicious Behavior ◽  
Byzantine Failures ◽  
Do So

The emergence of blockchains has fueled the development of resilient systems that can deal with Byzantine failures due to crashes, bugs, or even malicious behavior. Recently, we have also seen the exploration of sharding in these resilient systems, this to provide the scalability required by very large data-based applications. Unfortunately, current sharded resilient systems all use system-specific specialized approaches toward sharding that do not provide the flexibility of traditional sharded data management systems. To improve on this situation, we fundamentally look at the design of sharded resilient systems. We do so by introducing BYSHARD, a unifying framework for the study of sharded resilient systems. Within this framework, we show how two-phase commit and two-phase locking ---two techniques central to providing atomicity and isolation in traditional sharded databases---can be implemented efficiently in a Byzantine environment, this with a minimal usage of costly Byzantine resilient primitives. Based on these techniques, we propose eighteen multi-shard transaction processing protocols. Finally, we practically evaluate these protocols and show that each protocol supports high transaction throughput and provides scalability while each striking its own trade-off between throughput, isolation level, latency , and abort rate. As such, our work provides a strong foundation for the development of ACID-compliant general-purpose and flexible sharded resilient data management systems.

Circadian clock made in lab to probe biological rhythms

2021 ◽  
Vol 251 (3356) ◽  
pp. 15
Author(s):  
Jason Arunn Murugesu
Keyword(s):  
Circadian Clock ◽  
Biological Rhythms ◽  
Made In

scholarly journals EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock

2020 ◽  
Author(s):  
Zihao Zhu ◽  
Marcel Quint ◽  
Muhammad Usman Anwer
Keyword(s):  
Circadian Clock ◽  
Biological Rhythms ◽  
Early Flowering ◽  
Climate Change Scenarios ◽  
Temperature Changes ◽  
Physiological Processes ◽  
Average Global Temperature ◽  
Clock Component ◽  
Rhythmic Growth

SummaryPredictable changes in light and temperature during a diurnal cycle are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue, especially in light of climate change scenarios. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as an essential light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator was unable to properly respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.

scholarly journals Daily rhythms in gene expression of the human parasite Schistosoma mansoni

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Kate A. Rawlinson ◽  
Adam J. Reid ◽  
Zhigang Lu ◽  
Patrick Driguez ◽  
Anna Wawer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Schistosoma Mansoni ◽  
Circadian Clock ◽  
Drug Targets ◽  
Clock Genes ◽  
Biological Rhythms ◽  
Active Phase ◽  
Egg Laying ◽  
Daily Rhythms ◽  
Metazoan Parasites

Abstract Background The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis. Results Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity. Conclusions There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis.

scholarly journals Questions about household consumption in surveys

2007 ◽  
Vol 54 (3) ◽  
pp. 347-357
Author(s):  
Mirko Savic
Keyword(s):  
Household Consumption ◽  
General Purpose ◽  
Total Expenditure ◽  
Precise Information ◽  
Research Areas ◽  
Important Phenomenon ◽  
Do So ◽  
Valid Information

Household total expenditure (consumption) is a very important phenomenon in many research areas. The problem is how to get precise information about the consumption from each household and at the same time not to make the questionnaire so long and involved that it becomes a burden to the respondent. In this paper is evidence from several sources on the usefulness of recall consumption questions. Valid information can be collected by adding specific recall questions to general purpose surveys. There are a few recommendations on how to do so.

scholarly journals Integration of Nonlinear Models of Flexible Body Deformation in Multibody System Dynamics

2013 ◽  
Vol 9 (1) ◽  
Author(s):  
Martin Schulze ◽  
Stefan Dietz ◽  
Bernhard Burgermeister ◽  
Andrey Tuganov ◽  
Holger Lang ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Multibody System ◽  
Nonlinear Models ◽  
Equations Of Motion ◽  
Flexible Structures ◽  
General Purpose ◽  
Cosserat Rod ◽  
Rod Model ◽  
Flexible Deformation ◽  
Run Up

Current challenges in industrial multibody system simulation are often beyond the classical range of application of existing industrial simulation tools. The present paper describes an extension of a recursive order-n multibody system (MBS) formulation to nonlinear models of flexible deformation that are of particular interest in the dynamical simulation of wind turbines. The floating frame of reference representation of flexible bodies is generalized to nonlinear structural models by a straightforward transformation of the equations of motion (EoM). The approach is discussed in detail for the integration of a recently developed discrete Cosserat rod model representing beamlike flexible structures into a general purpose MBS software package. For an efficient static and dynamic simulation, the solvers of the MBS software are adapted to the resulting class of MBS models that are characterized by a large number of degrees of freedom, stiffness, and high frequency components. As a practical example, the run-up of a simplified three-bladed wind turbine is studied where the dynamic deformations of the three blades are calculated by the Cosserat rod model.

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