Related papers: Modeling compartmentalization within intracellular…
In this paper, a diffusion-based molecular communication channel is modeled in presence of a probabilistic absorber. The probabilistic absorber is an absorber which absorbs molecules upon collision with probability q. With random walk…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
In a diffusion-based molecular communication network, transmitters and receivers communicate by using signalling molecules (or ligands) in a fluid medium. This paper assumes that the transmitter uses different chemical reactions to generate…
Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by their cell membrane. Particle engulfment involves particle recognition by cell-surface receptors, signaling and remodeling of the actin…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
This article reviews the mechanical bidomain model, a mathematical description how the extracellular matrix and intracellular cytoskeleton are coupled by integrin proteins. The fundamental hypothesis is that differences between…
We consider two volume-surface reaction-diffusion systems arising from cell biology. The first system describes the localisation of the protein Lgl in the asymmetric division of Drosophila SOP stem cells, while the second system models the…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
The present study focuses on the receptor driven endocytosis typical of viral entry into a cell. A locally increased density of receptors at the time of contact between the cell and the virus is necessary in this case. The virus is…
Experiments on particles' motion in living cells show that it is often subdiffusive. This subdiffusion may be due to trapping, percolation-like structures, or viscoelatic behavior of the medium. While the models based on trapping (leading…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
A surrogate model for particle-in-cell plasma simulations based on a graph neural network is presented. The graph is constructed in such a way as to enable the representation of electromagnetic fields on a fixed spatial grid. The model is…
We derive and simulate a mathematical model for mechanotransduction related to the Rho GTPase signalling pathway. The model addresses the bidirectional coupling between signalling processes and cell mechanics. A numerical method based on…
Membrane transporters contribute to the regulation of the internal environment of cells by translocating substrates across cell membranes. Like all physical systems, the behaviour of membrane transporters is constrained by the laws of…
We investigate a recently proposed cross-diffusion system modelling the growth of gliobastoma taking into account size exclusion both in the migration and proliferation process. In addition to degenerate nonlinear cross-diffusion the model…
Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is…