Macromolecular crowding affects the activity of proteins and functional macromolecular
complexes in all cells, including bacteria. Crowding, together with physicochemical …

Molecular self-organziation, also regarded as pattern formation, is crucial for the correct
distribution of cellular content. The processes leading to spatiotemporal patterns often …

Most cellular processes depend on intracellular locations and random collisions of
individual protein molecules. To model these processes, we developed algorithms to …

In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation
to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from …

In E. coli, MinD recruits MinE to the membrane, leading to a coupled oscillation required for
spatial regulation of the cytokinetic Z ring. How these proteins interact, however, is not clear …

We introduce the software package ReaDDy for simulation of detailed spatiotemporal
mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with …

Min-protein oscillations in Escherichia coli are characterized by the remarkable robustness
with which spatial patterns dynamically adapt to variations of cell geometry. Moreover …

Motivation Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule
of interest as an individual particle in continuous space, simulating molecular diffusion …

Spatial stochastic simulation is a valuable technique for studying reactions in biological
systems. With the availability of high‐performance computing (HPC), the method is poised to …

Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical
trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction …