Related papers: Finding the positive feedback loops underlying mul…
It has been known for nearly a decade that deterministically modeled reaction networks that are weakly reversible and consist of a single linkage class have trajectories that are bounded from both above and below by positive constants (so…
The emergence and impact of tipping points have garnered significant interest in both the social and natural sciences. Despite widespread recognition of the importance of feedbacks between human and natural systems, it is often assumed that…
We consider the problem of optimizing the steady state of a dynamical system in closed loop. Conventionally, the design of feedback optimization control laws assumes that the system is stationary. However, in reality, the dynamics of the…
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…
Understanding the function of network motifs in an attempt to gain insight into how their combinations create larger reaction networks that drive cellular functions, has been a longstanding pursuit of systems biology. One specific objective…
In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…
Most complex systems are nonlinear, relying on emergent behavior from interacting subsystems, often characterized by oscillatory dynamics. Collective oscillatory behavior is essential for the proper functioning of many real world systems.…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and…
Dynamical entities interacting with each other on complex networks often exhibit multistability. The stability of a desired steady regime (e.g., a synchronized state) to large perturbations is critical in the operation of many real-world…
Oscillatory dynamics are ubiquitous in biological networks. Possible sources of oscillations are well understood in low-dimensional systems, but have not been fully explored in high-dimensional networks. Here we study large networks…
Many biological systems dynamically rearrange their components through a sequence of configurations in order to perform their functions. Such dynamic processes have been studied using network models that sequentially retrieve a set of…
Control theory arose from a need to control synthetic systems. From regulating steam engines to tuning radios to devices capable of autonomous movement, it provided a formal mathematical basis for understanding the role of feedback in the…
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…
Unstoppable feedback loops and tipping points in socio-ecological systems are the main threats to sustainability. These behaviors have been extensively studied, notably to predict, and arguably deviate, dead-end trajectories. Behind the…
Output feedback stabilization of control systems is a crucial issue in engineering. Most of these systems are not uniformly observable, which proves to be a difficulty to move from state feedback stabilization to dynamic output feedback…
Traditional percolation theory assumes static microscopic rules, limiting its ability to describe real-world complex systems where macroscopic order actively regulates local interactions. Here, we introduce feedback percolation, an unified…
"Dynamic compensation" is a robustness property where a perturbed biological circuit maintains a suitable output [Karin O., Swisa A., Glaser B., Dor Y., Alon U. (2016). Mol. Syst. Biol., 12: 886]. In spite of several attempts, no fully…
Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…
We present a model of adaptive regulatory networks consisting of a simple biologically-motivated rewiring procedure coupled to an elementary stability criterion. The resulting networks exhibit a characteristic stationary heavy-tailed degree…