At FAHcon 2012, Dr. Xuhui Huang presented our recent results of the molecular mechanisms of gene transcription. Transcription is the first step in reading genomic DNA, and regulation of this process plays a key role in cell differentiation and other fundamental processes. Misregulation of transcription is a major factor in cancer and other human diseases. Our simulation results are able to provide dynamic information for the transcription, and this dynamic information is largely inaccessible to present experimental techniques