ReaDDy – The Library for Reaction Diffusion Dynamics

by Johannes Schöneberg and Frank Noé



ReaDDy Logo Simulation:

The logo simulation mimicks a population growth process that frequently occurs in biology, e.g. bacteria colony growth. Sometimes, this growth process is subjected to spatial constraints, e.g. nutrients and bacteria are separated by a barrier. There are three different particle types, referring to that biological model:

  • Type 1, the redlogo particles“, serve as the spatial barriers. They have been given an attraction potential between them and start in a position that resembles the ReaDDy logo.
  • Type 2, the whitenutrient generators“. They can switch between a white ‘off‘ and an to a green an ‘on‘ state in which they can generate small “nutrient” particles.
  • Type 3, the light blue “bacterium” particles. Bacterium particles can consume “nutrients”. This changes their state and appearance. The more “nutrients” they consume, the larger they become. First, after 2 consumed “nutrient” particles, they become blue colored “bacteria lvl 2“, after 5, violet colored “bacteria lvl 3” and after 7, large, purple “bacteria lvl 4“. When a 10th “nutrient” is consumed, the “level 4 bacteria” split up into four new small level 0 bacteria and the cycle starts again.

It is visible during the time course of the simulation, that the spatial distribution of the particles, their crowding inducing occurrence in masses as well as spatial constraints like barriers influence the growth of the bacteria population dramatically. What is true for this simplified example is ubiquitous not only in molecular and cellular biology but in multiple other fields.

ReaDDy has been designed to fit the modeling requirements of such processes: Particle (or agent) based reaction diffusion systems in which particle-particle interactions play an important role and where the systems are subjected to crowding or spatial constraints.

The ReaDDy Logo simulation has been simulated with ReaDDy version 1.0 . Despite the biological model described above, the lengh-scales used in the simulation are derived from a molecular scale in the nanometer range, rather than from a micrometer range that would resemble the bacteria scenario. The qualitative observations about the capabilities of ReaDDy should not be affected by that. The simulation is done on a 2D plane of 1000×500 nm. In the beginning, it consists of 455 particles, diffusing with different diffusion constants, e.g. the slow “logo particles” diffuse at 0.2 µm²/s, the fast “nutrient” particles diffuse at 10 µm²/s. All particle types have different sizes. These are enforced by particle repulsion potentials that act between all particles and prevent particle-particle overlaps. In total the simulation consists of 500 000 timesteps of length 1ns and took about 5 hours to compute on a single core.