A system for corneal treatment, comprising: an illumination system 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 (A) reactions involving reactive oxygen species (ROS), and (B) 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 , wherein, in response to the determination of the at least one set of treatment parameters , the illumination system 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 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 (A) reactions involving reactive oxygen species (ROS), and (B) 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 , 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 (A) reactions involving reactive oxygen species (ROS), and (B) 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 , wherein, in response to the determination of the at least one set of treatment parameters , the illumination system 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. <EOS>