Growing Brains in Silico: Integrating Biochemistry, Genetics and Neural Activity in Neurodevelopmental Simulations

Biologists' understanding of the roles of genetics, biochemistry and activity in neural function is rapidly improving. All three interact in complex ways during development, recovery from injury and in learning and memory. The software system NeuroGene was written to simulate neurodevelopmental processes. Simulated neurons develop within a 3D environment. Protein diffusion, decay and receptor-ligand binding are simulated. Simulations are controlled by genetic information encoded using a novel programming language mimicking the control mechanisms of biological genes. Simulated genes may be regulated by protein concentrations, neural activity and cellular morphology. Genes control protein production, changes in cell morphology and neural properties, including learning. We successfully simulate the formation of topographic projection from the retina to the tectum. We propose a novel model of topography based on simulated growth cones. We also simulate activitydependent refinement, through which diffuse connections are modified until each retinal cell connects to only a few target cells.