Related papers: Promoter methylation in a mixed feedback loop circ…
We study a model consisting of $N$ nonlinear oscillators with {\em global periodic} coupling and {\em local multiplicative} and additive noises. The model was shown to undergo a nonequilibrium phase transition towards a broken-symmetry…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
Predator-prey models have been shown to exhibit resonance-like behaviour, in which random fluctuations in the number of organisms (demographic noise) are amplified when their frequency is close to the natural oscillatory frequency of the…
The ability of a circadian system to entrain to the 24-hour light-dark cycle is one of its most important properties. A new tool, called the entrainment map, was recently introduced to study this process for a single oscillator. Here we…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
The temporal behaviour of segmentation clock oscillations show phase synchrony via mean field like coupling of delta protein restricting to nearest neighbours only, in a configuration of cells arranged in a regular three dimensional array.…
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To…
Using the model of a generalized Van der Pol oscillator in the regime of subcritical Hopf bifurcation we investigate the influence of time delay on noise-induced oscillations. It is shown that for appropriate choices of time delay either…
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of…
By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415 (2005)).…
Common models of circadian rhythms are constructed as compartmental reactions of well mixed biochemicals involving a negative-feedback loop containing several intermediate reaction steps in order to enable oscillations. Spatial transport of…
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains,…
The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental…
Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely,…
Temperature compensation is a notable property of circadian oscillators that indicates the insensitivity of the oscillator system's period to temperature changes; the underlying mechanism, however, is still unclear. We investigated the…
Rhythms in electrical activity in the membrane of cells in the suprachiasmatic nucleus (SCN) are crucial for the function of the circadian timing system, which is characterized by the expression of the so-called clock genes. Intracellular…
Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…