Our work focuses on techniques for understanding the structure and response of complex, non-periodic systems, such as those encountered in energy research. Our methods include real-space, real time approaches for calculating electronic, vibrational, and thermal properties. We have also developed user friendly codes for such calculations, which are in use world-wide in physics, chemistry, biochemistry, geophysics. These methods are often used in energy research, e.g., understanding of catalytic materials. Our work provides a practical link between advanced theory and modern computational tools which are widely used by many scientists.