I will review our research activities that address the many new challenges of petroleum and coal industry. Our main efforts involve (1) flow assurance issues for deepwater oil production, (2) heavy oil upgrading and production, (3) coal conversion, (4) CH activation – application for low temperature gas to liquid conversion, (5) emulsion and surfactant technologies for enhanced oil recovery, and (6) advanced modeling of geochemistry and geochemical reactions. Using both theoretical and experimental approaches, quantitative models have been developed for the above problems. In the presentation, I will emphasize in particular how we have used successfully molecular modeling technology for these engineering problems, such as (1) corrosion issues, (2) scale dissolution, (3) catalysis for CH activation, (4) low temperature heavy oil upgrading, (5) wax inhibition, (6) wear inhibition, (7) emulsion and oil water interfacial tension modeling, (8) using ionic liquid to facility alkylation process and (9) geochemical modeling for subsurface geochemical reactions.