Probing Protein/DNA Transcription Machinery via Physical Modeling and Computational Interrogation 

Molecular machinery regulating gene transcription in central dogma consists of factor proteins and enzymes responsible for locating DNA promoter sequences and then initiating and elongating for DNA template-based synthesis of RNA. Implementing physical modeling and simulation from atomic to coarse-grained level, along with polymer physics model, statistic mechanics and stochastic kinetic/dynamics approaches, we have re-examined transcription factor diffusional search along DNA, explored RNA polymerase (RNAP) promoter recognition, characterized particularly the mechanochemical and fidelity control during RNAP elongation, and further probed DNA supercoiling as mechanical feedback of transcription. In particular, the backgrounds, central issues of interest, and significances of the researches are to be addressed.