Bonj, if you knew anything about metallurgy.....
Your bike will not be made of aluminium, but of an aluminium alloy, of which there are many. One example of such an alloy is Dural, which in essence is an alu-copper alloy. This affects the yield point, work-hardening and other aspects of the material. Your bike, if it is worth anything, should also have steel inserts at certain points, such as the drop outs, as alu is softer than steel and more likely to deform under such things as axle nut compression.
It is not the molecules in your frame material that are likely to change. A piece of metal is not a crystalline matrix, but an amalgam of grains. It is common metallurgical practice to take a cross section of a sample and polish it smooth at one end to reveal the granular structure. This structure can change under, in particular, cyclic stresses such as flex, or, importantly, cyclic compression such as happens every time you turn your pedals while riding. This is cyclic compression, NOT flex, and can lead to fatigue failure. Stress meters/strain guages can record microscopic movement that you would not detect as flex.
Such cyclic stresses can alter the structure and arrangement of the metal's granular structure. They can, for example, initiate cracks. Such microscopic cracks can propagate, and with stress concentration at areas such as joints become major features leading to failure. That is why a decently engineered frame should have smooth radius curves, not sharp corners.
