The transportation and information gathering needs of our world are changing. Transportation systems are becoming more vital for our society and also more congested. Networking holds out the hope for more efficient use of multiple autonomous systems but also opens the door for increased risk exposure to failures and malicious attacks. Developments in internet technologies, online auctions and games, social networks, high-technology engineered systems with multiple dynamic components, and elsewhere motivate new advancements for decision, interaction, and control in cyberphysical systems (CPS) with autonomous dynamical subsystems. Examples of vehicle CPS can be found in areas as diverse as automobiles, air transportation, civil infrastructure, trains, and surface and subsurface water vehicles. Information Assurance must provide authentic, accurate, secure, reliable, and timely information to vehicle decision and control systems in order to achieve information dominance, mission performance, and survivability in risky changing environments. Computing and information processes must be carried out over distributed and heterogeneous networked systems for resilience to minimize single point of failure to malicious attacks. Recent advances in autonomous cyberphysical systems show promise for improved reconnaissance, surveillance, and security in foreign and domestic conflicts. However, CPS also present new and unevaluated sets of attack surfaces in communications and controls. As such, the modeling and simulation of cyber security in autonomous systems is a critical research area that will ultimately dictate the ways these systems should interact with people and each other. Thus, the goal of this Special Issue is collect a comprehensive body of descriptive and prescriptive approaches to modeling and simulating cyber security threats, defense techniques, and overall frameworks in highly dynamic and hostile environments. This special issue is composed of five papers that show the current state of modeling, simulation, decision, and control in some important areas of cyberphysical systems. The paper by Yagdereli, Gemci, and Aktas x presents a study on cyber security of unmanned vehicles, including cars, civilian unmanned aircraft, trains, and boats. Types of cyber-attacks are characterized, including passive and active attacks. Potential vulnerabilities of autonomous vehicles are detailed. Metrics for cybersecurity are proposed. A framework for mitigation strategies based on modeling and simulation is presented. The paper by Bergin presents a cyber-attack and simulation framework based on a live-virtual-constructive (LVC) environment. The focus is on wireless mobile network interfaces for military autonomous vehicles. LVC offers opportunities for training and assessment of humanin-the loop performance. Security threats and vulnerabilities are discussed, and attack techniques are outlined including denial of service, passive attack, and malicious agents. A cyber-attack and simulation framework is detailed including methods of data modeling, storage, and transfer. The paper by Cavagnaro and Tiller presents a framework for risk assessment of force allocation and countermeasures in autonomous vehicle air operations. A probability theory approach is used to define tipping points to quantify game outcomes that represent mission success. Probability distributions are presented for risk assessment, and random walks are employed to yield a distribution of outcome results. Based on these tools, the Tiller software wargame simulation Modern Air Power has been developed and is applied in this paper to force allocation and countermeasures based on game-changing capabilities.