Gemstones and Crystals were living creatures millions of years ago. They emit certain fundamental rhythmic frequencies/vibrations when they are subjected to light, heat, electricity and pressure.
Dhyana Yoga incorporates "Crystal/Gem-Therapy" during the meditation where crystals are placed on energy centers of the body. Crystals starts vibrating due to body temperature, mantra chanting and bioelectric activity and emits certain rhythmic frequencies which helps to boost the energy nodes in the body. Energy vibration created by the Crystals influences towards positive mindset.