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We introduce a simple procedure of multivariate signal analysis to uncover the functional connectivity among cells composing a living tissue and describe how to apply it for extracting insight on the effect of drugs in the tissue. The…
The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial…
We consider here a single-compartment model of these neurons which is capable of describing many of the known features of spike generation, particularly the slow rhythmic pacemaking activity often observed in these cells in a variety of…
Polyelectrolytes, such as polyacrylic acid (PAA), can effectively mitigate $\mathrm{CaCO_3}$ scale formation. Despite their success as antiscalants, the underlying mechanism of $\mathrm{Ca^{2+}}$ binding to polyelectrolyte chains remains…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
The complex dynamics of intracellular calcium regulates cellular responses to information encoded in extracellular signals. Here, we study the encoding of these external signals in the context of the Li-Rinzel model. We show that by control…
Calcium and reactive oxygen species (ROS) interact with each other and play an important role in cell signaling networks. Based on the existing mathematical models, we develop an age-dependent feedback control model to simulate the…
The presynaptic free calcium dynamics of neurons due to various stimulation protocols is investigated in a mathematical model. The model includes calcium influx through voltage-dependent calcium channels, calcium buffering by endogenous and…
Toxoplasma gondii is the causative agent responsible for toxoplasmosis and serves as one of the most common parasites in the world. For a successful lytic cycle, T. gondii must traverse biological barriers in order to invade host cells, and…
Biochemical signaling cascades transmit intracellular information while dissipating energy under nonequilibrium conditions. We model a cascade as a code string and apply information-entropy ideas to quantify an optimal transmission rate. A…
Plasma membrane calcium influx through ion channels is crucial for many events in cellular physiology. Cell surface stimuli lead to the production of inositol 1,4,5-trisphosphate (IP3), which binds to IP3 receptors in the endoplasmic…
Like many other biological processes, calcium dynamics in neurons containing an endoplasmic reticulum are governed by diffusion-reaction equations on interface-separated domains. Interface conditions are typically described by systems of…
Accurate regulation of calcium release is essential for cellular signaling, with the spatial distribution of ryanodine receptors (RyRs) playing a critical role. In this study, we present a nonlinear spatial network model that simulates RyR…
A stochastic model of intracellular calcium oscillations is analytically studied. The governing master equation is expanded under the linear noise approximation and a closed prediction for the power spectrum of fluctuations analytically…
We develop a spatially explicit biophysical model of the hippocampal CA3-CA1 presynaptic bouton to study local calcium dynamics leading to vesicle fusion. A kinetic model with two calcium sensors is formulated specifically for the CA3-CA1…
In embryogenesis, epithelial cells, acting as individual entities or as coordinated aggregates in a tissue, exhibit strong coupling between chemical signalling and mechanical responses to internally or externally applied stresses.…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
Photoplethysmogram (PPG) and electrocardiogram (ECG) are commonly recorded in intesive care unit (ICU) and operating room (OR). However, the high incidence of poor, incomplete, and inconsistent signal quality, can lead to false alarms or…
This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the…
The epileptic mechanism is postulated as that an animal's neurons gradually diminish their inhibition function coupled with enhanced excitation when an epileptic event is approaching. Calcium imaging technique is designed to directly record…