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Its normally that case that most material modeling techniques rely on energy minimizations, which result in the equilibrium solutions for most chemical of physical processes. While this is great for the general case, most things in life rely on disequilibrium to drive reactions/processes. One big field that uses disequilibrium chemistry for modeling reactions is Exoplanet Atmospheric Modeling, here you can see a general idea of how its used in said field.

What are some ways to model these disequilibrium processes with current software packages? As a bonus follow-up if you personal use disequilibrium processes in your research; how and why is it used?

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To study system on disequilibrium, just apply the wanted conditions and run the calculations under such conditions. For example, Prof. Oganov (developer of USPEX software) has very interesting studies about NaCl at high pressures, methane on Neptune (pdf) and other materials under extreme conditions, all in disequilibrium conditions.

Particularly, one of my research lines is rational drug design. One of the methodology I use is to study the interactions of small molecules with proteins. In this case, I study, for example, the electronic properties in equilibrium (isolated molecule) and after interacting with the protein (out of equilibrium).

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