Cell-free protein synthesis (CFPS), an experimental method for conducting in vitro protein synthesis, has distinct advantages over conventional recombinant in vivo expression. Compared to traditional protein synthesis techniques, CFPS is notably less time consuming (with experiments lasting only hours versus days or weeks), enables direct manipulation of the chosen system, and reduces toxicity concerns commonly associated with extraneous enzymatic interactions. Producing complex eukaryotic proteins has continued to be a source of scientific frustration in the field of proteomics. The proper folding and optimal synthesis of complex proteins is a limitation that is shared by recombinant in vivo expression systems and cell-free in vitro methods of protein expression. Since this issue is exhibited in both techniques of laboratory-controlled protein expression; it may be possible that current representations of the eukaryotic protein synthesis process, as it occurs in nature, may not be modeled accurately. Protein synthesis models and laboratory expression techniques have traditionally concentrated on the effects of chemical-manipulation and genetic changes; however, contemporary studies suggest that environmental, thermodynamic, kinetic, and mechanical stimuli are also particularly important regulators of eukaryotic gene transcription. The cellular nucleus, where transcription occurs, serves as the scaffold for necessary signal transduction pathways involved in transcription. The transduction of various stimuli to biochemical signals may alter nuclear morphology, the intranuclear distribution of nucleic acids, and transcription/replication processes because the nucleus acts as a highly sensitive mechanosensor. Therefore, if the nucleus remains intact in a sample lysate utilized for eukaryotic CFPS then the transcriptional plasticity of the system may become altered due to deformations in the nuclear architecture caused by laboratory manipulations (such as an adjustment in the composition of the extracellular matrix, fluctuation of mechanical stimuli levels [e.g., the mechanical perturbation required to induce cell lysis], and modulation of the thermodynamic and kinetic properties of load-bearing macromolecules). Therefore, in order to fully benefit from the advantages provided by CFPS, the focus of this study will entail an exploration and dimensional analysis of the parameters (e.g., environmental, chemical, thermodynamic, kinetic, mechanical stimuli, etc.) that influence naturally occurring and laboratory manipulated methods of eukaryotic protein synthesis. The development of detailed mathematical models for the major processes involved in eukaryotic protein synthesis (e.g. transcription, translation, and protein folding) will advance our understanding of eukaryotic protein expression and provide a foundation for a similarity analysis of the protein expression processes in the in vivo (non-recombinant/naturally occurring) and in vitro systems. Ultimately, the results of the similarity analysis may produce a model for CFPS that represents the natural process more accurately; thus, the CFPS system may be able to be optimized to achieve improved products and product yields.