Lipid confined systems, such as organelles or lipid‐based delivery carriers, play a pivotal role in human health and disease, which makes them highly significant to biotechnology research. While modern imaging techniques can reach nanometer‐scale resolution, they provide only static snapshots and must be complemented by approaches capable of capturing dynamic structural changes in a lipid confined system. Molecular dynamics (MD) simulations can address this need by offering up to atomistic detail at femtosecond resolution and enabling access to dynamics on timescales up to milliseconds, thereby complementing the experimental data. With the rapid growth of high‐performance computing capabilities, accessible temporal and spatial scales are expanding, bringing the era of computational microscopy within reach. In this article, we highlight the key challenges that remain on the path toward this vision. We overview model construction protocols based on a modular building‐block approach, together with dynamic 3D time‐resolved data extraction, analysis, and visualization workflows. Such strategies will allow the scientific community to fully exploit high‐performance computing resources and move closer to a truly computational microscopy era. With these tools in hand, MD simulations will significantly broaden their utility for experimentalists, not only in visualization but also in high throughput computational screening and experiment design.
Čechová et al. (Sun,) studied this question.