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A celebrated and controversial hypothesis conjectures that some biological systems --parts, aspects, or groups of them-- may extract important functional benefits from operating at the edge of instability, halfway between order and…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
Learning models or control policies from data has become a powerful tool to improve the performance of uncertain systems. While a strong focus has been placed on increasing the amount and quality of data to improve performance, data can…
Many crucial biological processes operate with surprisingly small numbers of molecules, and there is renewed interest in analyzing the impact of noise associated with these small numbers. Twenty--five years ago, Berg and Purcell showed that…
Recent experimental results point to the existence of coherent quantum phenomena in systems made of a large number of particles, despite the fact that for many-body systems the presence of decoherence is hardly negligible and emerging…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
Birhythmicity arises in several physical, biological and chemical systems. Although, many control schemes are proposed for various forms of multistability, only a few exist for controlling birhythmicity. In this paper we investigate the…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Exerting fluctuations is a part of our daily life: traffic noise, heartbeat, opinion poll, currency exchange rate, electrical current, chemical reactions - they all permanently fluctuate. One of the most important questions is why the…
A model of interacting random walkers is presented and shown to give rise to patterns consisting in periodic arrangements of fluctuating particle clusters. The model represents biological individuals that die or reproduce at rates depending…
We show explicitly the entropy reduction from a detailed fluctuation theorem for the general stochastic system driven by nonequilibrium process under feedback control. The effect of interaction of the feedback controller with the system is…
In many areas of engineering and sciences, decision rules and control strategies are usually designed based on nominal values of relevant system parameters. To ensure that a control strategy or decision rule will work properly when the…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Stochasticity is a defining feature of the pairwise forces governing interactions in biological systems-from molecular motors to cell-cell adhesion-yet its consequences on large-scale dynamics remain poorly understood. Here, we show that…
To maintain renewing epithelial tissues in a healthy, homeostatic state, (stem) cell divisions and differentiation need to be tightly regulated. Mechanisms of homeostatic control often rely on crowding control: cells are able to sense the…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
Response time-delay is an ubiquitous phenomenon in biological systems. Here we use a simple stochastic population model with time-delayed switching-rate conversion to quantitatively study the biological influence of the response time-delay…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
Coherent oscillatory activity can arise spontaneously as a result of increased coupling in a system of excitable and passive cells, each being quiescent in isolation. This can potentially explain the appearance of spontaneous rhythmic…