The use of self-assembling peptide hydrogels in the treatment of spinal cord and brain injuries, especially when combined with adult neural stem cells, has shown great potential. To advance tissue engineering, it is essential to understand the effect of mechanochemical signaling on cellular differentiation. The elucidation of the molecular interactions at the level of the neuronal membrane still represents a promising area of investigation for many drug delivery and tissue engineering applications. An innovative molecular dynamics framework has been introduced to investigate the effect of SAP fibrils with different charges on neural membrane lipid domain dynamics. Such advance enables the in silico exploration of the biomimetic properties of SAP hydrogels and other polymeric biomaterials for tissue engineering applications.