亚细胞过程
Receptor-ligand binding is a critical first step in signal transduction and the duration of the interaction can impact signal generation. In mammalian cells, clustering of receptors may be facilitated by heterogeneous zones of lipids, known…
We use Monte Carlo simulations to study attractive and excluded volume interactions between nucleosome core particles in 30 nm-chromatin fibers. The nucleosomes are treated as disk-like objects having an excluded volume and short range…
We show that at the onset of a cyclic fold bifurcation, a birhythmic medium composed of glycolytic oscillators displays turbulent dynamics. By computing the largest Lyapunov exponent, the spatial correlation function, and the average…
T cells form intriguing patterns during adhesion to antigen-presenting cells. The patterns at the cell-cell contact zone are composed of two types of domains, which either contain short TCR/MHCp receptor-ligand complexes or the longer…
The recent discovery of a lateral organization in cell membranes due to small structures called 'rafts' has motivated a lot of biological and physico-chemical studies. A new experiment on a model system has shown a spectacular budding…
Mobility of taxol inside microtubules was investigated using fluorescence recovery after photobleaching (FRAP) on flow-aligned bundles. Bundles were made of microtubules with either GMPCPP or GTP at the exchangeable site on the tubulin…
The biogenesis of lipid droplets (LD) in the yeast Saccharomyces cerevisiae was theoretically investigated on basis of a biophysical model. In accordance with the prevailing model of LD formation, we assumed that neutral lipids oil-out…
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular…
The problem of \emph{statistical recognition} is considered, as it arises in immunobiology, namely, the discrimination of foreign antigens against a background of the body's own molecules. The precise mechanism of this…
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…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
The mean time for a diffusing ligand to activate a target protein located on the surface of a microdomain can regulate cellular signaling. When the ligand switches between various states induced by chemical interactions or conformational…
The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing…
"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address…
FADD (Fas-associated death domain) is the main death receptor adaptor molecule that transmits apoptotic signal. Recently, FADD protein was shown to be expressed both in the cytoplasm and nucleus of in vitro cell lines. In contrast to the…
We model the self-organization of the MinE ring that is observed during subcellular oscillations of the proteins MinD and MinE within the rod-shaped bacterium {\it Escherichia coli}. With a steady-state approximation, we can study the…
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
Previous studies have described the concept of peptide strings in qualitative terms and illustrated it by applying its corrolaries in order to elucidate basic questions in oncology and rheumatology. The present investigation is the first to…
While ordinary differential equations (ODEs) form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The most common formulation of stochastic…
The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in,…