In this study, we use density functional theory (DFT) at a micro-level and laboratory experiments at a macro-level to understand two phenomena: the molecular mechanisms responsible for the chemical aging of asphalt, and the restorative effect of a new generation of bio-modifiers for treating aged asphalt. Our DFT-based studies show that the interplay of a series of competing factors is responsible for enhancement of the intermolecular interactions in aged (oxidized) asphaltene dimers compared to unaged (unoxidized) forms. While electron-withdrawing groups of carbonyl (C= O) around the aromatic core decrease the spatial extent of the p-electron cloud and unfavorable repulsion interaction, they reduce the electron density and subsequently reduce some favorable non-covalent interactions in this region. The loss of electrostatic quadrupole-quadrupole interactions in the aromatic center is partially compensated for by new forms of electrostatic interactions in another part of the molecule. Next, we use a modifier derived from animal waste to rejuvenate the oxidized asphaltenes. DFT results show that the main components of the bio-rejuvenator are able to mitigate the effect of polar substitutions generated through oxidation. Interestingly, the chemical nature of asphaltenes in our bio-rejuvenator is dramatically different from asphaltenes of aged or unaged asphalt. The FTIR picture of the bio-rejuvenator asphaltenes shows the aromatic cores with shorter aliphatic side chains and many more ether and hydroxyl side groups. HRTEM images confirm the disturbance of the aged asphaltene agglomerates and enchantment the lattice spacing in the presence of the target bio-rejuvenator.