Abstract: Protein factors and enzymes can work as nanometer-scale machinery that achieves sophisticated function inside cells. Understanding how the microscopic machinery operates precisely can inform rational molecular design and biomedical applications. We have investigated transcription factor (TF) and RNA polymerase (RNAP) as the most important protein machinery regulating gene transcription (DNA to RNA), where errors can lead to genome instability or cancer. We use physics-based modeling, atomic to coarse-grained simulation, and machine learning to investigate how proteins locate their targets on DNA. We have also probed viral and related RNAPs, elucidating their structural dynamics with dimension-reduction analyses. The combined computational studies are expected to enhance biophysical understanding of how protein machinery operate or potentially malfunction, to support biomolecular engineering and anticancer/antiviral developments.