Frequent pipe filling in intermittent and other pipe systems may result in extreme transient flow conditions mainly caused by the formation and destruction of two-phase flows. This thesis aims at providing insights into select issues associated with rapid pipe filling, including water column separation and rejoinder, a more complete physical understanding of rapid pressurization of the pipe systems containing entrapped air, and improvements in the numerical modeling of transient mixed flow in pipelines. Through an extensive numerical exploration, this thesis identifies three new sources of water column separation which can produce extensive water hammer pressures. The underlying physics associated with these findings are explained, and the sensitivity of the resulting water hammer pressures to the different parameters of pipe systems is revealed. The key challenges of experiments with this dynamic event are identified and a test rig is proposed. Numerical exploration also reveals that air valves can modify water column separation, but they can, on the other hand, result in a column separation-like event if they are not sized properly. This work also proposes an energy auditing approach under light of which the complex physics associated with rapid pressurization of pipe systems with entrapped air can be readily explained. This approach is successfully applied to a variety of problems. Finally, the causes of the numerical instability associated with the Preissmann Slot Method -- issues that have been a challenge for over four decades -- are explored and a new non-oscillatory numerical model is shown to be able to completely remove the numerical instability issue even when high waves speeds are modeled.
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