An effective security of today"s transportation infrastructures is difficult to achieve without computer-aided approach. In this book, we develop a set of security-enhancing computational methods for transportation infrastructures with many independent agents, motivated by scenarios of contemporary maritime piracy, border patrol, and drug trafficking. We model these problems within the game-theoretic framework as a zero-sum game between a defending player and an intruding player. We extend iterative oracle-based techniques allowing computation of Nash Equilibria of games with a very large number of strategies. We step outside the game-theoretic framework when considering multiple transiting agents transiting the infrastructure and we propose a grouping mechanism to group the agents together during the area transit, taking their speeds and risk aversion into account. Finally, we present a computational model of the maritime transportation system in a form of an agent-based simulation....