Transcription, the synthesis of RNA from a complementary DNA template, plays a crucial role in cellular regulation, including differentiation, development, and other fundamental processes. In this talk, I will discuss our results on modeling the RNA polymerase II (Pol II, a system with ~400K atoms) Translocation and other functional conformational changes of this enzyme at sub-millisecond timescales. We have developed a novel algorithm, Hierarchical Nystrom Extension Graph method, to construct kinetic network models to extract long timescale dynamics from short simulations. For example, we reveal that RNA polymerase II translocation is driven purely by thermal energy and does not require the input of any additional chemical energy. Our model shows an important role for the bridge helix: Large thermal oscillations of this structural element facilitate the translocation by specific interactions that lower the free-energy barriers between four metastable states. The dynamic view of translocation presented in our study represents a substantial advance over the current understanding based on the static snapshots provided by X-ray structures of transcribing complexes. At the end of my talk, I will briefly discuss our recent progress on extending our kinetic network model to include sequence-dependent molecular dynamics of Pol II elongation to predict transcriptional accuracy in the genome-wide transcriptomic datasets. This model creates a critical link between the structural-mechanics understanding of Pol II fidelity and the genome-wide transcriptional accuracy.