Related papers: The stochastic behavior of a molecular switching c…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
Bistability and multistationarity are properties of reaction networks linked to switch-like responses and connected to cell memory and cell decision making. Determining whether and when a network exhibits bistability is a hard and open…
The ultimate spatial limit to establish a Josephson coupling between two superconducting electrodes is an atomic-scale junction. The Josephson effect in such ultrasmall junctions has been used to unveil new switching dynamics, study…
Homeostasis is a running theme in biology. Often achieved through feedback regulation strategies, homeostasis allows living cells to control their internal environment as a means for surviving changing and unfavourable environments. While…
A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It…
We study decoherence in a qubit with the distance between the two levels affected by random flips of bistable fluctuators. For the case of a single fluctuator we evaluate explicitly an exact expression for the phase-memory decay in the echo…
We show that the thermodynamic limit of a bistable phosphorylation-dephosphorylation cycle has a selection rule for the "more stable" macroscopic steady state. The analysis is akin to the Maxwell construction. Based on the chemical master…
We undertake a detailed numerical study of the twin phenomena of stochastic and vibrational resonance in a discrete model system in the presence of bichromatic input signal. A two parameter cubic map is used as the model that combines the…
Diverse complex dynamical systems are known to exhibit abrupt regime shifts at bifurcation points of the saddle-node type. The dynamics of most of these systems, however, have a stochastic component resulting in noise driven regime shifts…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
Multiple interlinked positive feedback loops shape the stimulus responses of various biochemical systems, such as the cell cycle or intracellular calcium release. Recent studies with simplified models have identified two advantages of…
Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…
The two-state Togashi-Kaneko model demonstrates how, at finite system sizes, autocatalysis can lead to noise-induced bistability between the cellular concentrations of different molecular species. Here, we show that, in the biologically…
This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely…
The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…
We demonstrate and contrast two approaches to the stabilization of qubit entanglement by feedback. Our demonstration is built on a feedback platform consisting of two superconducting qubits coupled to a cavity which are measured by a…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Protein nanoclustering is a characteristic feature of their activated state and is essential for forming numerous subcellular structures. The formation of these nanoclusters is highly dependent on a series of post-translational…
The competition between interactions and dissipative processes in a quantum many-body system can drive phase transitions of different order. Exploiting a combination of cluster methods and quantum trajectories, we show how the systematic…
We consider the stochastic patterns of a system of communicating, or coupled, self-propelled particles in the presence of noise and communication time delay. For sufficiently large environmental noise, there exists a transition between a…