Consistent time-dependent modeling of microphysics becomes increasingly desired by emerging astrophysical research. In this talk, I will introduce the need for these simulations, and our efforts to implement Microthena, the GPU-accelerated numerical infrastructures for microphysics. Their applications in the research of protoplanetary disks (PPDs) will be discussed. I will emphasize the comprehensive, thermochemistry-coupled dynamics of PPDs, in the modeling of photoevaporative and/or MHD-dominated wind-launching dispersal processes. With these tools, our discoveries in exoplanetary atmospheres will also be presented, including our proposed model of "super-puff" exoplanets. Moreover, our current efforts of conducting cosmological simulations on Microthena are expected to shed light on currently unresolved "sub-grid physics" and hence to prepare for intensity mapping observations of the upcoming decade. These simulations, with their rich details in thermochemical profiles, are promising for future attempts to bridge current theoretical models to observations.