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This is really interesting. Apparently physical activity increases white matter integrity. White matter consists of cells and axons that are responsible for communication between the different parts of the brain. The axons in the white matter work best if they are myelinated which means a fatty layer forms around them. This allows nerve cells to transmit information faster. It seems that physical activity increases this proces of myelination which leads to increased cognitive and academic performance.

http://www.psychologytoday.com/blog/the-athletes-way/201409/why-is-physical-activity-so-good-your-brain