A system for corneal treatment, comprising: an illumination system (110, 112) configured to deliver photoactivating light to a cross-linking agent applied to a cornea, the photoactivating light generating cross-linking activity with the cross-linking agent; and a controller including one or more processors and computer-readable storage media, the controller configured to receive input relating to a desired biomechanical change in the cornea and to execute, with the one or more processors, program instructions stored on the storage media to: determine, from a photochemical kinetic model, a three-dimensional distribution of cross-links for the cornea to achieve the desired biomechanical change in the cornea, the photochemical kinetic model calculating the distribution of cross-links based on cross-linking from reactions involving reactive oxygen species, and reactions not involving oxygen, and determine at least one set of treatment parameters to achieve the distribution of cross-links, the at least one set of treatment parameters including illumination parameters for the delivery of the photoactivating light by the illumination system (110, 112), wherein, in response to the determination of the at least one set of treatment parameters, the illumination system (110, 112) is configured to deliver the photoactivating light to the cornea according to the illumination parameters, characterized in that: the ROS include at least peroxides, superoxides, and hydroxyl radicals. an illumination system (110, 112) configured to deliver photoactivating light to a cross-linking agent applied to a cornea, the photoactivating light generating cross-linking activity with the cross-linking agent; and a controller including one or more processors and computer-readable storage media, the controller configured to receive input relating to a desired biomechanical change in the cornea and to execute, with the one or more processors, program instructions stored on the storage media to: determine, from a photochemical kinetic model, a three-dimensional distribution of cross-links for the cornea to achieve the desired biomechanical change in the cornea, the photochemical kinetic model calculating the distribution of cross-links based on cross-linking from reactions involving reactive oxygen species, and reactions not involving oxygen, and determine at least one set of treatment parameters to achieve the distribution of cross-links, the at least one set of treatment parameters including illumination parameters for the delivery of the photoactivating light by the illumination system (110, 112), determine, from a photochemical kinetic model, a three-dimensional distribution of cross-links for the cornea to achieve the desired biomechanical change in the cornea, the photochemical kinetic model calculating the distribution of cross-links based on cross-linking from reactions involving reactive oxygen species, and reactions not involving oxygen, and determine at least one set of treatment parameters to achieve the distribution of cross-links, the at least one set of treatment parameters including illumination parameters for the delivery of the photoactivating light by the illumination system (110, 112), wherein, in response to the determination of the at least one set of treatment parameters, the illumination system (110, 112) is configured to deliver the photoactivating light to the cornea according to the illumination parameters, characterized in that: the ROS include at least peroxides, superoxides, and hydroxyl radicals.