Im on Ubuntu 13.10, Free Brain version 188.8.131.52, J-1.7.0_51.
I rarely reboot my system and I leave Brain on most of the time to add constant notes. If it sits over night by the middle of the next day its slowed to a crawl and takes upwards of 5 min to change between thoughts. Im running 12GB of ram with more than 50% free on a multi-core system. Even if I turn off all other software on my system over night, by mid morning the next day, it will be so slow and finally freezes. The only way to exit out is to open Resource Manager and kill java.