Related papers: Biological implications of dynamical phases in non…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic…
When complex systems are driven to extinction by some external factor, their non-stationary dynamics can present an intermittent behaviour between relative tranquility and burst of activity whose consequences are often catastrophic. To…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
We describe a new complex system model of an evolving production economy. This model is the simplest we can envisage which incorporates the new observation that the rate of an economic production process depends only on the minimum of its…
Biomolecular condensates in cells are often rich in catalytically-active enzymes. This is particularly true in the case of the large enzymatic complexes known as metabolons, which contain different enzymes that participate in the same…
Phase transitions and critical behavior of driven systems are reviewed. Models exhibiting phase transitions, spontaneous symmetry breaking, phase separation and coarsening processes in d=1 dimension are discussed.
Biological synaptic transmission is unreliable, and this unreliability likely degrades neural circuit performance. While there are biophysical mechanisms that can increase reliability, for instance by increasing vesicle release probability,…
Due to the processes that occur during the functioning of modern electromechanical systems, these systems can be considered complex nonlinear dynamic systems from the point of view of the theory of dynamic systems. The movement of such…
We review theory of information thermodynamics which incorporates effects of measurement and feedback into nonequilibrium thermodynamics of a small system, and discuss how the second law of thermodynamics should be extended for such…
We study the evolution of a random weighted network with complex nonlinear dynamics at each node, whose activity may cease as a result of interactions with other nodes. Starting from a knowledge of the micro-level behaviour at each node, we…
Dynamical systems theory describes how interacting quantities change over time and space, from molecular oscillators to large-scale biological patterns. Such systems often involve nonlinear feedbacks, delays, and interactions across scales.…
With the aim of understanding the emergence of collective motion from local interactions of organisms in a "noisy" environment, we study biologically inspired, inherently non-equilibrium models consisting of self-propelled particles. In…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Flow networks are essential for both living organisms and enginneered systems. These networks often present complex dynamics controlled, at least in part, by their topology. Previous works have shown that topologically complex networks…
Maxwell's demon elucidates the value of information in thermodynamics, using measurement and feedback: he evolves an equilibrated gas into a nonequilibrium state, from which one might extract work. The demon can evolve the system farther…
The study of stochastic systems has received considerable interest over the years. Their dynamics can describe many equilibrium and nonequilibrium fluctuating systems. At the same time, nonequilibrium constraints interact with the time…
We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective…
The Mpemba effect, an example of anomalous thermal relaxations, occurs when a system prepared at a hot temperature overtakes an identical system prepared at a warm temperature and cools down faster to the environment's temperature. We study…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…