The progress of nano-technology enables us to manipulate bio-molecules directly on the substrate. In particular, recent development in chemical treatment of solid surfaces and nano-fabrication on them provides a variety of fine controlled substrates. Surface condition of the nano-controlled substrate is critically important for the handling of bio-molecules such as proteins, nucleotide acids, lipid, glycan etc. The compatibility between solid surfaces and bio-molecules, in other words bio-interface, is a key factor for the success in interdisciplinary study of nano-technology and biology. With increasing performance of computers, it has become a possible and practical research target to analyze the interfacial interaction between bio-molecules and solid surfaces. The findings from the computational study are helpful for interpreting experimental results and enhance the understanding of the interface phenomena. Further, theoretical approach will be indispensable for the design of bio-solid interface. In this paper, we demonstrate the advantage of collaborative approach between experiments and computation, exemplifying several studies to analyze the behavior of proteins on the surface.