Understanding physicochemical interactions during biokinetic regulation will be critical for the creation of relevant nanotechnology supporting cellular and molecular engineering. The impact of nanoscale influences in medicine and biology can be explored in detail through mathematical models as an in silico testbed. In a recent single-cell biomechanical analysis, the cytoskeletal strain response due to fluid-induced stresses was characterized (Wilson, Z. D., and Kohles, S. S., 2010, “Two-Dimensional Modeling of Nanomechanical Strains in Healthy and Diseased Single-Cells During Microfluidic Stress Applications,” J. Nanotech. Eng. Med., 1(2), p. 021005). Results described a microfluidic environment having controlled nanometer and piconewton resolution for explorations of multiscale mechanobiology. In the present study, we constructed a mathematical model exploring the nanoscale biomolecular response to that controlled microenvironment. We introduce mechanical stimuli and scaling factor terms as specific input values for regulating a cartilage molecule synthesis. Iterative model results for this initial multiscale static load application have identified a transition threshold load level from which the mechanical input causes a shift from a catabolic state to an anabolic state. Modeled molecule homeostatic levels appear to be dependent upon the mechanical stimulus as reflected experimentally. This work provides a specific mathematical framework from which to explore biokinetic regulation. Further incorporation of nanomechanical stresses and strains into biokinetic models will ultimately lead to refined mechanotransduction relationships at the cellular and molecular levels.