Brownian motion particles with reactions and membranes simulator. To try it out go to https://www.hermanbergwerf.com/bromium-deploy/ and press the refresh button (third from the top-left).
Bromium consists of the following set of smaller libraries:
bromium.mathCollection of general mathematical algorithms
bromium.viewsAdditional typed views
bromium.structsData structures for the simulation
bromium.kineticsSimulation kinetics algorithms
bromium.nodesLibrary for node based scene modeling
bromium.engineController for an isolated simulation with nodes
bromium.rendererSimulation 3D renderer
It is discouraged to add sanity checks to data structures (for example to detect impossible reactions). This makes the code more complex and less readable. Instead the code should be more resilient towards incorrect data.
In almost all circumstances it is preferred to use types from the
library to keep the code more readable. Array to vector conversion should be
Prefer for-in loops over forEach loops. For-in loops look cleaner and are not officially closures.
Use final in for loops when possible (e.g.
for (final thing in things)). Do
not use final in method or function arguments. These are almost always final and
adding final to all final arguments would add a lot of code. Besides, it's not a
common practice to add final to arguments.
Meaningless comments such as
/// Constructor or copied comments from the
super class should be omitted.
Error messages should be full sentences.
Topics for further research
Optimization of reaction finding
Currently a voxel based approach is used where all inter-voxel reactions are implicitly discarded. Alternative approaches have shown significant lower performance. More performance might be gained by caching results from previous cycles, or by using a different voxel number computation such as a Z-order curve. A very interesting question is how much the voxel approach hurts the accuracy of the entire simulation.
Accuracy of brownian motion
Currently a not too accurate approach is used to compute the random motion. Each cycle the particle is displaced by a normalized vector that points in a random direction times a random number between 0 and 1.
Membrane protein motion
Membrane proteins can be simulated using sticky particles. Currently there is no implementation to simulate membrane protein dynamics. The amount of motion that should be applied to sticky particles to simulate accurate membrane dynamics has yet to be researched.