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Inspired by nature, it is envisaged that a nanorough surface exhibits bactericidal properties by rupturing bacterial cells. In order to study the interaction mechanism between the cell membrane of a bacteria and a nanospike at the contact point, a finite element model was developed using the ABAQUS software package. The model, which saw a quarter of a gram-negative bacteria (Escherichia coli) cell membrane adhered to a 3 × 6 array of nanospikes, was validated by the published results, which show a reasonably good agreement with the model. The stress and strain development in the cell membrane was modeled and were observed to be spatially linear and temporally nonlinear. From the study, it was observed that the bacterial cell wall was deformed around the location of the nanospike tips as full contact was generated. Around the contact point, the principal stress reached above the critical stress leading to a creep deformation that is expected to cause cell rupture by penetrating the nanospike, and the mechanism is envisaged to be somewhat similar to that of a paper punching machine. The obtained results in this project can provide an insight on how bacterial cells of a specific species are deformed when they adhere to nanospikes, and how it is ruptured using this mechanism.