Related papers: Amplified biochemical oscillations in cellular sys…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
A formalism is developed which describes the extent to which stochastic oscillations in biochemical models are synchronised. It is based on the calculation of the complex coherence function within the linear noise approximation. The method…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic.…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
As biochemical systems may frequently suffer from limited energy resources so that internal molecular fluctuation has to be utilized to induce random rhythm, it is still a great theoretical challenge to understand the elementary principles…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
In this work we focus on how noise propagates in biochemical reaction networks and affects sensitivities of the system. We discover that the stochastic fluctuations can enhance sensitivities in one region of the value of control parameters…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
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…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…