Related papers: Biochemical Oscillations in Delayed Negative Cycli…
Despite widespread and striking examples of physiological oscillations, their functional role is often unclear. Even glycolysis, the paradigm example of oscillatory biochemistry, has seen questions about its oscillatory function. Here, we…
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…
Oscillator models are central to the study of system properties such as entrainment or synchronization. Due to their nonlinear nature, few system-theoretic tools exist to analyze those models. The paper develops a sensitivity analysis for…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
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,…
This paper deals with the phase noise affecting communication systems, where local oscillators are employed to obtain reference signals for carrier and timing synchronizations. The most common discrete-time phase noise channel model is…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Biochemical oscillations are ubiquitous in living organisms. In an autonomous system, not influenced by an external signal, they can only occur out of equilibrium. We show that they emerge through a generic nonequilibrium phase transition,…
In many real-world oscillator systems, the phase response curves are highly heterogeneous. However, dynamics of heterogeneous oscillator networks has not been seriously addressed. We propose a theoretical framework to analyze such a system…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
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…
Systems of dynamical elements exhibiting spontaneous rhythms are found in various fields of science and engineering, including physics, chemistry, biology, physiology, and mechanical and electrical engineering. Such dynamical elements are…
An important design principle for biological oscillators divides the oscillators into two classes: fixed frequency, variable amplitude and fixed amplitude, variable frequency. Because of the interplay of nonlinearity and feedback, both…
Periodic patterns in dynamical behaviours of biological models described by simple form differential delay equations are studied. Mathematical models are given by a class of scalar delay differential equations with a multiplicative time…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Self-organized network dynamics prevails for systems across physics, biology and engineering. How external signals generate distributed responses in networked systems fundamentally underlies their function, yet is far from fully understood.…
Bioreactors are widely used in many industries to generate a range of products using various host cells e.g., yeast, insect, and mammalian cells. Depending on the process, product, and host cell, some bioreactors exhibit sustained periodic…
In an oscillatory medium, a region which oscillates faster than its surroundings can act as a source of outgoing waves. Such pacemaker-generated waves can synchronize the whole medium and are present in many chemical and biological systems,…
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…