Energy

"Thanks to your nano-systems, you are not entirely organic. If an EMP weapon hits you, your bio energy reserves will be drained severely."

- description of EMP Damage

Being machines, both the heavy machinery used in Mechanical Augmentation and the Nanites used in Nano Augmentation require a power source to function. Bio energy is the electrical energy that powers these devices. In Deus Ex and Deus Ex: Invisible War, the player has internal "batteries" that contain a limited reserve of bio energy, and both using Augmentations and being hit by EMP Weapons will drain this reserve. When the Energy Meter is empty, the player cannot use augmentations. The player's bio energy can be replenished through the use of Power cells, but the Power Recirculator aug can conserve the amount of energy used.

In Deus Ex the Matsu-Gravas R-118 Repair bot can be used to recharge a characters energy supply on request. (75%)

In Deus Ex: Invisible War the Piezochem W31V Repair bot can be used to recharge a characters energy supply automatically. (100%)

In Deus Ex: Human Revolution Adam must consume energy bars or paste to replenish his energy cells, with only the first of a possible five energy cells automatically recharging.

Triva
A conversation between Walton Simons and Jaime Reyes suggests that if a augmented person keeps their bioenenrgy at 100% for long periods of time they may experience an intermittent sharp pain behind their eyes.