Related papers: Protein sequestration versus Hill-type repression …
We study the impact of light on the mammalian circadian system using the theory of phase response curves. Using a recently developed ansatz we derive a low-dimensional macroscopic model for the core circadian clock in mammals.…
Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in…
The cosinor model is frequently used to represent the oscillatory behavior of different genes over time. When data are collected from multiple individuals, the cosinor model is estimated with recorded gene expression levels and the 24 hour…
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,…
Small continuous sensory and mechanical perturbations have often been used to identify properties of the closed-loop neural control of posture and other systems that are approximately linear time invariant. Here we extend this approach to…
We consider controller design for robust output tracking and disturbance rejection for continuous-time periodic linear systems with periodic reference and disturbance signals. As our main results we present four different controllers: A…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
Circadian rhythmicity lies at the center of various important physiological and behavioral processes in mammals, such as sleep, metabolism, homeostasis, mood changes and more. It has been shown that this rhythm arises from self-sustained…
During cell division paired (sister) chromosomes are observed to perform approximate saw-tooth oscillations across the cell mid-plane. Experimental data suggests that these oscillations are regulated through intersister tension. We propose…
A model of Drosophila circadian rhythm generation was developed to represent feedback loops based on transcriptional regulation of per, Clk (dclock), Pdp-1, and vri (vrille). The model postulates that histone acetylation kinetics make…
There are many different types of time keeping devices. We use the phrase ticking clock to describe those which -- simply put -- "tick" at approximately regular intervals. Various important results have been derived for ticking clocks, and…
A biophysical model of arousal dynamics is used to study mechanisms of synchronisation and loss of synchrony among the three key oscillators controlling sleep-wake cycles: the circadian, homeostatic, and light oscillators. Synchronisation…
The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale…
In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene circuit with three genes that cyclically repress transcription of the next gene--as well as a corresponding mathematical model. Experimental data and model…
Epilepsy is a common, chronic neurological disorder characterized by recurrent seizures caused by sudden bursts of abnormal electrical activity in the brain. Seizures can often be unpredictable, leading to uncertainty and anxiety for people…
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…
Measuring time means counting the occurrence of periodic phenomena. Over the past centuries a major effort was put to make stable and precise oscillators to be used as clock regulators. Here we consider a different class of clocks based on…
Atomic frequency standards have achieved steadily increasing precision over the past seventy years, enabled in part by feedback mechanisms that stabilise their output. In parallel, the timekeeping capabilities of quantum systems have been…
The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and…