The Transactions on Computational Science journal is part of the Springer series Lecture Notes in Computer Science, and is devoted to the gamut of computational science issues, from theoretical aspects to application-dependent studies and the va- dation of emerging technologies. The current issue is devoted to computer systems research and the application of such research, which naturally complement each other. The issue is comprised of Part 1: Computational Visualization and Optimization, and Part 2: Computational Methods for Model Design and Analysis. Part 1 - Computational Visualization and Optimization - is devoted to state-of-the-art research carried out in this area with the use of novel computational methods. It is c- prised of five papers, each addressing a specific computational problem in the areas of shared virtual spaces, dynamic visualization, multimodal user interfaces, computational geometry, and parallel simulation, respectively. Part 2 - Computational Methods for Model Design and Analysis - continues the topic with an in-depth look at selected computational science research in the areas of data representation and analysis. The four papers comprising this part cover such areas as efficient reversible logic design, missing data analysis, stochastic computation and neural network representation for eccentric sphere models. Each paper describes a detailed experiment or a case study of the methodology presented to amplify the impact of the contribution.