Related papers: An allosteric model of the inositol trisphosphate …
We give a review of the current state of the art of data-driven modelling of the inositol trisphosphate receptor (IPR). After explaining that the IPR plays a crucial role as a central regulator in calcium dynamics, several sources of…
We present a novel nonlinear state transition model for inositol 1,4,5-trisphosphate receptors (IP$_3$Rs) that incorporates a pre-activated state, as suggested by electron microscopy observations. Our model provides a theoretical framework…
Clusters of IP3 receptor channels in the membranes of the endoplasmic reticulum (ER) of many non-excitable cells release calcium ions in a cooperative manner giving rise to dynamical patterns such as Ca2+ puffs, waves, and oscillations that…
We focused our attention on Ca$^{2+}$ release from the endoplasmic reticulum through a cluster of inositol 1,4,5-trisphosphate (IP$_3$) receptor channels. The random opening and closing of these receptors introduce stochastic effects that…
The calcium (Ca$^{2+}$) signalling system is important for many cellular processes within the human body. Signals are transmitted within the cell by releasing Ca$^{2+}$ from the endoplasmic reticulum (ER) into the cytosol via clusters of…
Intracellular calcium is regulated in part by the release of Ca$^{2+}$ ions from the endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP$_3$R) channels (among other possibilities such as RyR and L-type calcium channels). The…
Many of the processes that underly neural computation are carried out by ion channels embedded in the plasma membrane, a two-dimensional liquid that surrounds all cells. Recent experiments have demonstrated that this membrane is poised…
The cystic fibrosis transmembrane conductance regulator (CFTR) is an important membrane protein in vertebrates. The function of CFTR is to transport chloride ions across the cell membrane, which is known to require adenosine triphosphate…
G-protein-coupled receptors (GPCRs) are central to cellular information processing, yet the physical principles governing their switching behavior remain incompletely understood. We present a first principles theoretical framework, grounded…
Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signalling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors (RyRs) for cellular contraction,…
Recent years have witnessed an increasing interest in neuron-glia communication. This interest stems from the realization that glia participates in cognitive functions and information processing and is involved in many brain disorders and…
Intracellular Ca signals represent a universal mechanism of cell function. Messages carried by Ca are local, rapid, and powerful enough to be delivered over the thermal noise. A higher signal to noise ratio is achieved by a cooperative…
We present a general framework for incorporating non-reciprocal interactions into the Ising model with Glauber dynamics, without requiring multiple species. We then focus on a model with vision-cone type interactions. We solve it in a fully…
Many cell types exhibit oscillatory activity, such as repetitive action potential firing due to the Hodgkin-Huxley dynamics of ion channels in the cell membrane or reveal intracellular inositol triphosphate (IP$_3$) mediated calcium…
Accurate forecasting of industrial time series requires balancing predictive accuracy with physical plausibility under non-stationary operating conditions. Existing data-driven models often achieve strong statistical performance but…
Atomic isotope shifts (ISs) are the isotope-dependent energy differences in the atomic electron energy levels. These shifts serve an important role in atomic and nuclear physics, and particularly in the latter as signatures of nuclear…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B connected via a linker C. The existing ISAPT algorithm displays…
Recently, it has been suggested that ion channel selectivity filter may exhibit quantum coherence, which may be appropriate to explain ion selection and conduction processes. Potassium channels play a vital role in many physiological…
Integrated Sensing and Communication (ISAC) has been identified as a key 6G application by ITU and 3GPP. A realistic, standard-compatible channel model is essential for ISAC system design. To characterize the impact of Sensing Targets…