Diffuse axonal injury (DAI), a major component of traumatic brain injury, is a manifestation of microstructural cellular trauma and various ensuing neurochemical reactions that leads to secondary neuronal death. DAI is suggested to result from the initial increase in the membrane permeability caused by the mechanical forces acting on the axons. Permeability increases disturb ion balance and lead to cytoskeletal disruption resulting in the impairment of axonal transport. In this study, we present an in vitro neurotrauma model that reproduces important features of in vivo DAI such as membrane permeability changes, focal disruption of microtubules, impaired axonal transport, and focal axonal beading, the “hallmark” morphology of DAI. In addition, we show that the post-injury increase in the intracellular calcium ion concentration and subsequent calpain activity are the underlying phenomena in the neuropathological sequelae following mechanical injury. Interestingly, calcium and calpain activity are pronounced in focal “hot spots” that develop into axonal beads. Post-injury application of Poloxamer 188, a polymer known to reseal damaged membranes, successfully reduced mechanoporation, calpain activity, microtubule disruption, and axonal beading. These results suggest that membrane repair has a therapeutic potential in DAI. We have developed a spatio- temporal axon model to simulate post-injury calcium and calpain mechanisms. We show that calcium-dependent calpain activity depends on the amount of poration and is modulated by mitochondria and calpain activation dynamics.