It is difficult for us to directly observe the digestion process of food in the human gastrointestinal tract. However, molecular simulation is a powerful tool for us to explore the unknown world. We wonder whether molecular simulation can visualize this process?
At the atomic level?, yes: bond formation/breaking can be simulated, and the free energy profile of the enzymatic reaction calculated, using, for example, the empirical valence bond approach, in which reactants, intermediates, and products are represented as valence-bond species, and the transition between them is calculated by the free energy perturbation approach.
Molecular simulations is a powerful tool for processes at atomic and molecular level, but you have to bear in mind that the length-scales and time-scales that are accessible for molecular simulations, provided you use supercomputers, are around a few tens of nm and ns-ms (small systems - longer time and viceversa). And then you have to have more precise questions before your set up the simulations (like "how protein A bonds to enzyme B" or something). Just throwing everything in a simulations box to see "what happens" is rarely a good idea.
I like your idea. It is important to implement it as correctly as possible. To do this, you need to clearly formulate the task. For example, modeling the digestion of proteins in the stomach is extremely problematic, because you do not define the processes that you are going to model. On other hand, you can quite successfully model the hydrolysis of a specific protein under the influence of hydrochloric acid of the stomach.
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