The development of modern biology has been made possible thanks to the widespread use of simulations that have enabled researchers to overcome the cognitive challenges in this field, such as the impact of performing measurements on the system being studied, the complexity of the system itself, and the difficulty of establishing certain properties through typical theoretical and experimental studies. Subcellular biology is of particular interest, because physical, chemical, and typically biological properties are all important at this level, making the problem of adequately understanding this reality one of the greatest cognitive challenges of modern science. For this reason, it is particularly important to critically examine the epistemology of computer simulations in biology. The novelty of this paper lies in a thorough discussion of the main determinants of using simulations in biology, with there being a particular emphasis on subcellular biology. It also identifies the main reasons for the growing epistemic distance between the reality being studied and the knowledge gained. This study is also important for understanding the epistemic foundations of biology in general and subcellular biology in particular, as well as contributing to the philosophical reflection on the role of computer simulations in modern science.