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Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in…
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…
High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…
Glutamate and glycine are important neurotransmitters in the brain. An action potential prop- agating in the terminal of a presynatic neuron causes the release of glutamate and glycine in the synapse by vesicles fusing with the cell…
Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…
Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…
A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to…
Muscle uses Ca2+ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca2+ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential,…
We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an…
Cells continuously probe their environment with membrane receptors, achieving subsecond adaptation of their behaviour [1-3]. Recently, several receptors, including cadherins, were found to bind ligands with a lifetime of order of one…
A qualitative model is presented, suggesting gravitational information is transduced into biological systems primarily by its effect on spatially organised membrane and cytoplasmic flows. Continuous low affinity interactions between…
A novel definition of the stimulus-specific information is presented, which is particularly useful when the stimuli constitute a continuous and metric set, as for example, position in space. The approach allows one to build the spatial…
Signaling events in eukaryotic cells are often guided by a scaffolding protein. Scaffold proteins assemble multiple proteins in a spatially localized signaling complex and exert numerous physical effects on signaling pathways. To study…
We propose a model for cell polarization as a response to an external signal which results in a system of PDEs for different variants of a protein on the cell surface and interior respectively. We study stationary states of this model in…
In this paper we show that living cells can multiplex biochemical signals, i.e. transmit multiple signals through the same signaling pathway simultaneously, and yet respond to them very specifically. We demonstrate how two binary input…
Scaffolding proteins that direct the assembly of multiple kinases into a spatially localized signaling complex are often essential for the maintenance of an appropriate biological response. Although scaffolds are widely believed to have…
Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
We examine the synchrony of the dynamics of localized [Ca^{2+}]_i oscillations in internal pool of astrocytes via diffusing coupling of a network of such cells in a certain topology where cytosolic Ca^{2+} and inositol 1,4,5-triphosphate…