Bromium

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).

Sub-libraries

Bromium consists of the following set of smaller libraries:

• bromium.math Collection of general mathematical algorithms
• bromium.views Additional typed views
• bromium.structs Data structures for the simulation
• bromium.kinetics Simulation kinetics algorithms
• bromium.nodes Library for node based scene modeling
• bromium.engine Controller for an isolated simulation with nodes
• bromium.renderer Simulation 3D renderer

Code conventions

Sanity checks

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.

Types

In almost all circumstances it is preferred to use types from the vector_math library to keep the code more readable. Array to vector conversion should be minimized.

Loops

Prefer for-in loops over forEach loops. For-in loops look cleaner and are not officially closures.

Final

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.

Comments

Meaningless comments such as /// Constructor or copied comments from the super class should be omitted.

Error messages

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.