There is growing evidence of the importance of mechanical deformations on various facets of cell functioning. This asks for a proper understanding of the cell’s characteristics as a mechanical system in different physiological and mechanical loading conditions. Many researchers use atomic force microscopy (AFM) indentation and the Hertz contact model for elastic material property identification under shallow indentation. For larger indentations, many of the Hertz assumptions are not inherently satisfied and the Hertz model is not directly useful for characterizing nonlinear elastic or inelastic material properties. We have used exponential hyperelastic material in FE simulations of the AFM indentation tests. A parameter identification approach is developed for hyperelastic material property determination from the simulated data. We collected AFM indentation data on agarose gel and developed a simple algorithm for contact point detection. The contact point correction improves the prediction of elastic modulus over the case of visual contact point identification. The modulus of 1% agarose gel was found to be about 15 kPa using the proposed correction, with mild but non-trival hardening with deeper indentation. The experimental data is compared with the results from the FE simulations and shows that over the hardening portion of the indentation response, our proposed parameter identification approach successfully captures the experimental data.

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