Related papers: Oscillations and temporal signalling in cells
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…
Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Spontaneous oscillations measured by Local field potentials (LFPs), electroencephalograms and magnetoencephalograms exhibits variety of oscillations spanning frequency band ($1-100$ Hz) in animals and humans. Both instantaneous power and…
Intracellular fluctuations, mainly triggered by gene expression, are an inevitable phenomenon observed in living cells. It influences generation of phenotypic diversity in genetically identical cells. Such variation of cellular components…
The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
We analyze a simple stochastic model to describe motor molecules which cooperate in large groups and present a physical mechanism which can lead to oscillatory motion if the motors are elastically coupled to their environment. Beyond a…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…
Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by…
We here study a network of synaptic relations mingling excitatory and inhibitory neuron nodes that displays oscillations quite similar to electroencephalogram (EEG) brain waves, and identify abrupt variations brought about by swift synaptic…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
Cortical oscillations are thought to be involved in many cognitive functions and processes. Several mechanisms have been proposed to regulate oscillations. One prominent but understudied mechanism is gap-junctional coupling. Gap junctions…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Oscillations of free intracellular calcium concentration are thought to be important in the control of a wide variety of physiological phenomena, and there is long-standing interest in understanding these oscillations via the investigation…
Circadian rhythms are archetypical examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are…
Thalamic relay cells fire action potentials that transmit information from retina to cortex. The amount of information that spike trains encode is usually estimated from the precision of spike timing with respect to the stimulus. Sensory…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…