Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics

Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics

The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and ST...

Reaction diffusion modeling of calcium dynamics with realistic ER geometry.

We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diff...

Diffusion Modeling of snRNP Dynamics

Small nuclear ribonucleoprotein particles (snRNPs) are essential supramolecular complexes mediating a process of pre-mRNA splicing. The particles undergo complex assembly steps in a highly dynamic nuclear compartment called the Cajal body. Since the dynamics of the assembly and a movement of snRNPs inside the nucleus is poorly understood, we tested the in vivo snRNP dynamics in the frame of a s...

Toward Biomolecular Computers Using Reaction-Diffusion Dynamics

Mesoscopic model for diffusion-influenced reaction dynamics.

A hybrid mesoscopic multiparticle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum, and energy so that hydrodynamic effects are fully taken into account. Reactive and nonreactive interactions with catalytic solute particles are described by full molecular dynamics. Results are presented for large-scale, three-dime...