Related papers: Oscillation patterns in negative feedback loops
Protein sequestration motifs appear in many biological regulatory networks and introduce special properties into the network dynamics. Sequestration can be described as a mode of inactivation of a given protein by its binding to a second…
We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of…
Networked dynamical systems, i.e., systems of dynamical units coupled via nontrivial interaction topologies, constitute models of broad classes of complex systems, ranging from gene regulatory and metabolic circuits in our cells to…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
Feedback optimization has emerged as an effective strategy for steady-state optimization of dynamical systems. By exploiting models of the steady-state input-output sensitivity, methods of this type are often sample efficient, and their use…
We consider the effects of temporal delay in a neural feedback system with excitation and inhibition. The topology of our model system reflects the anatomy of the avian isthmic circuitry, a feedback structure found in all classes of…
Lateral inhibition resulting from a double-negative feedback loop underlies the assignment of different fates to cells in many developmental processes. Previous studies have shown that the presence of time delays in models of lateral…
Motivated by the aim to find new medical strategies to suppress undesirable neural synchronization we study the control of oscillations in a system of inhibitory coupled noisy oscillators. Using dynamical properties of inhibition, we find…
Oscillations are omnipresent in neural population signals, like multi-unit recordings, EEG/MEG, and the local field potential. They have been linked to the population firing rate of neurons, with individual neurons firing in a…
It is well known that conservative mechanical systems exhibit local oscillatory behaviours due to their elastic and gravitational potentials, which completely characterise these periodic motions together with the inertial properties of the…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
One of the main features of adaptive systems is an oscillatory convergence that exacerbates with the speed of adaptation. Recently it has been shown that Closed-loop Reference Models (CRMs) can result in improved transient performance over…
The biologist Ren\'e Thomas conjectured, twenty years ago, that the presence of a negative feedback circuit in the interaction graph of a dynamical system is a necessary condition for this system to produce sustained oscillations. In this…
Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Many complex systems can spontaneously oscillate under non-periodic forcing. Such self-oscillators are commonplace in biological and technological assemblies where temporal periodicity is needed, such as the beating of a human heart or the…
The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are…
The feedback between mechanical and chemical signals plays a key role in controlling many biological processes and collective cell behavior. Here we focus on the emergence of spatiotemporal density waves in a one-dimensional "cell train."…