the pattern of microscopic bumps on neurons are dendritic spines:
http://en.wikipedia.org/wiki/Dendritic_spine. these have glutamate receptors.
Glutamate is the primary excitatory transmitter in the brain. The Glutamate synpase has two receptors: AMPA and NMDA. These act as an AND gate for learning and are both activated by glutamate.
When glutamate binds to the AMPA receptor, it opens a channel that lets in sodium (Na+). If enough enters fast enough, Mg+2 is reppelled from blockading the NMDA receptor allowing Ca+2 ions to enter.
http://en.wikipedia.org/wiki/Excitatory_postsynaptic_potenti...
When Ca+2 enters the cells through NMDA, it triggers a ton of internal metabolic changes. in the neuron in order to do make it more sensitive and conditioned to the connections from stimulating neurons such as producing more AMPA receptors at that location for example.
http://en.wikipedia.org/wiki/Hebbian_learning
We don't know all of the internal metabolic changes that allow the cell to do such things, and this article is about one of them.
Brief neurosci101 to put the article in perspective.