From 2013.igem.org

Notebook : July 17

Modeling

Meeting memo
Meeting Date: 17/07/2013
Meeting participants: Patrick Amar, Claire Toffano-Nioche, Abdou Mouhtare, Damir Damipator, Gabriel Gallin, Zhou Yi
Recorder: Zhou Yi

Hsim:
-Hsim is created for bio-chemical reaction simulation, it demonstrates bio-chemical systems which the scientists are already known.

-The molecules are simulated as spheres (in 2D or 3D). Initial positions and size of sphere are configurable.

-example of a Hsim command:
B + V -> R + V [probability]

-Molecules diffusion are simulated by movements of spheres, if the distance between two centers of the spheres is less than the sum of 2 radium, we consider that will lead to a collision.

-Computer takes a random sample and compare it to the probability which is specified in equation. If the value exceeds the threshold, we consider that the reaction takes place.

-Probability of success is associated with kinetics of reaction which depends on concentrations of molecules varying during the reaction.

-Time unit is 100ms. So movement of spheres is discreet.
-Spheres move randomly but could follow some stochastic rules (like Brownian movement).

Ethic about open source:
-Hsim is not an open source software, it belongs to the University of Paris Sud. However, it is a free software, we can download it free.