The two-volume set LNCS 5592 and 5593 constitutes the refereed proceedings of the International Conference on Computational Science and Its Applications, ICCSA 2009, held in Seoul, Korea, in June/July, 2009. The two volumes contain papers presenting a wealth of original research results in the field of computational science, from foundational issues in computer science and mathematics to advanced applications in virtually all sciences making use of computational techniques. The topics of the fully refereed papers are structured according to the five major conference themes: computational methods, algorithms and scientific applications, high performance technical computing and networks, advanced and emerging applications, as well as information systems and information technologies. Moreover, submissions from more than 20 workshops and technical sessions contribute to this publication. These cover topics such as geographical analysis, urban modeling, spatial statistics, wireless and ad hoc networking, logical, scientific and computational aspects of pulse phenomena in transitions, high-performance computing and information visualization, sensor network and its applications, molecular simulations structures and processes, collective evolutionary systems, software engineering processes and applications, molecular simulations structures and processes, internet communication security, security and privacy in pervasive computing environments, and mobile communications.