In such systems, the environment is considered to be at equilibrium. Hernandez, however, studies non-equilibrium reactions in which the reacting chemicals form a large part of the overall environment. In such systems, the environment changes as the reaction proceeds, affecting the chemistry in ways that are difficult to model and study. This complex interaction between reaction and changing environment affects the outcome in important ways. I want to understand how things are formed, not just to characterize their properties once they are formed.
Protein folding provides an important example.
After creation, proteins fold through a complex chemical process that involves as many as 200 different amino acid residues. Different folds give the proteins different properties. We as dynamicists are asking how a sequence with a given structure goes to that folded structure. By understanding those dynamics, we would be able to say something about altering the sequence and preventing it from folding that way. A supercomputer model accounting for complex changes in reactants and environment may provide answers that researchers could find in no other way.