相关论文: Bifurcation analysis of a model of the budding yea…

Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…

The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the…

Yeast cells produce daughter cells through a DNA replication and mitosis cycle associated with checkpoints and governed by the cell cycle regulatory network. To ensure genome stability and genetic information inheritance, this regulatory…

A living cell is an open, nonequilibrium biochemical system where ATP hydrolysis serves as the energy source for a wide range of intracellular processes, possibly including the assurance for decision-making. In the fission yeast cell cycle,…

Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…

Cellular differentiation in a developping organism is studied via a discrete bistable reaction-diffusion model. A system of undifferentiated cells is allowed to receive an inductive signal emenating from its environment. Depending on the…

To maintain a constant cell size, dividing cells have to coordinate cell cycle events with cell growth. This coordination has for long been supposed to rely on the existence of size thresholds determining cell cycle progression [1]. In…

Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…

Ordinary differential equations (ODEs) can model the transition of cell states over time. Bifurcation theory is a branch of dynamical systems which studies changes in the behavior of an ODE system while one or more parameters are varied. We…

Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…

Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…

We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…

Fission yeast G2/M transition is regulated by a biochemical reaction networks which contains four components: Cdc13, Cdc2, Wee1, and Cdc25. This circuit is characterized by the ultrasensitive responses of Wee1 or Cdc25 to Cdc13/Cdc2…

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle…

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example, and show that its transition paths are…

Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and…

Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…

We perform a bifurcation analysis of the mathematical model of Jones and Kompala [K.D. Jones and D.S. Kompala, Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures, J. Biotech., 71:105-131,…

When bacteria are grown on a mixture of two growth-limiting substrates, they exhibit a rich spectrum of substrate consumption patterns including diauxic growth, simultaneous consumption, and bistable growth. In previous work, we showed that…