HVAC systems are very important to our wellbeing, energy, and the environment. Current design tools are typically supported by basic knowledge, and keep us at arm's length from the many practical problems. The design paradigm has been shifted several times in the past from thermal comfort, energy conservation, health concerns, and now probably to security issues. Each of the shift has required better design tools of HVAC systems.A team led by Dr. Jelena Srebric at the Department of Architecture, the Penn State University (PSU) is developing new HVAC design tools to meet the new challenges on building security. A recent research effort is to couple computational fluid dynamics modeling with multi-zone modeling for reliable and fast indoor environment simulations. New models have been developed for complicated boundary conditions such as air supply diffusers and dynamic wall temperatures, and they have been validated by laboratory and on-site measurements. Simulations have been successfully conducted for buildings with displacement ventilation, chilled ceilings and high induction diffusers. As outdoor environment can strongly influence indoor one, we are developing a new turbulence model for fast simulations of outdoor contaminant dispersion. Some other related research will also be discussed.